HG38 to CHM13v2 VCF liftover using chain
jamesdalg opened this issue · 6 comments
jamesdalg commented
I'm having some issues lifting over using the provided chain files. GATK complains that it can't find the reference sequence, yet I'm not precisely sure why. If you know of a workaround, let me know. I'm using GATK version 4.2.4.1, java 17.0.2, and picard 2.26.9.
(base) [dalgleishjl@cn0848 ~]$ ls -l /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa
-rw-r-----. 1 dalgleishjl CCRBioinfo 26337875 May 10 12:09 /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa
(base) [dalgleishjl@cn0848 ~]$ java -jar $PICARD_JAR LiftoverVcf I=/fdb/GATK_resource_bundle/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz O=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/CHM13v2.0.known_indels.vcf CHAIN=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/hg38-chm13v2.over.chain R=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa REJECT=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/CHM13v2.0.known_indels.NOT_LIFTED_OVER.vcf;
INFO 2022-05-19 18:59:59 LiftoverVcf
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** LiftoverVcf -I /fdb/GATK_resource_bundle/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz -O /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/CHM13v2.0.known_indels.vcf -CHAIN /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/hg38-chm13v2.over.chain -R /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa -REJECT /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/CHM13v2.0.known_indels.NOT_LIFTED_OVER.vcf
**********
19:00:00.005 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/apps/picard/2.26.9/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu May 19 19:00:00 EDT 2022] LiftoverVcf INPUT=/fdb/GATK_resource_bundle/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz OUTPUT=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/CHM13v2.0.known_indels.vcf CHAIN=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/hg38-chm13v2.over.chain REJECT=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/CHM13v2.0.known_indels.NOT_LIFTED_OVER.vcf REFERENCE_SEQUENCE=/data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Thu May 19 19:00:00 EDT 2022] Executing as dalgleishjl@cn0848 on Linux 3.10.0-862.14.4.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 17.0.2+8-LTS-86; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.26.9
INFO 2022-05-19 19:00:01 LiftoverVcf Loading up the target reference genome.
[Thu May 19 19:00:02 EDT 2022] picard.vcf.LiftoverVcf done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=754974720
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Reference sequence (1) not found in /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa
at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:104)
at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:334)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
(base) [dalgleishjl@cn0848 ~]$ ls -l /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa
-rw-r-----. 1 dalgleishjl CCRBioinfo 26337875 May 10 12:09 /data/CCRBioinfo/dalgleishjl/sv_mapping/chm13_ref/chm13v2.0.fa
jamesdalg commented
Also, if there is an alternative set of tools that will do the same job, I'm open to that as well.
diekhans commented
You might try crossmap: http://crossmap.sourceforge.net/
I haven't used it, but have heard good things
Manoswini-02 commented
@jamesdalg have you checked the chromosome notation of all the given files? They have to be same for proper mapping.
It looks like one of your input files might have chromosome notation as numerals.
I tried running the same and in my case, it ran without any error but nothing has lifted over and the reject file is huge.
jamesdalg commented
@Manoswini-02 Maybe you have a different version of that file. I don't see that issue with the file I have on our HPC cluster. See below:
-bash-4.2$ gzcat /fdb/GATK_resource_bundle/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz | head -n 1000000 | tail -n 100
chr8 110098448 1369907 C CGT . PASS set=variant2
chr8 110098724 . ATAT A 131.63 PASS set=variant2
chr8 110100058 rs112172286 ATTAT A 12833.07 PASS AC=198;AF=0.09;AFR_AF=0.28;AMR_AF=0.04;AN=2184;ASN_AF=0.07;AVGPOST=0.9966;ERATE=0.0005;EUR_AF=0.01;LDAF=0.0900;RSQ=0.9867;THETA=0.0003;VT=INDEL;set=Intersection
chr8 110101681 . CAAAT C 168 PASS AC=20;AF=0.01;AFR_AF=0.04;AMR_AF=0.0028;AN=2184;AVGPOST=0.9978;ERATE=0.0003;LDAF=0.0098;RSQ=0.9192;THETA=0.0002;VT=INDEL;set=variant
chr8 110102567 . AG A 21 PASS AC=83;AF=0.04;AFR_AF=0.09;AMR_AF=0.02;AN=2184;ASN_AF=0.03;AVGPOST=0.9334;ERATE=0.0096;EUR_AF=0.02;LDAF=0.0574;RSQ=0.5363;THETA=0.0003;VT=INDEL;set=variant
chr8 110102568 rs67482162,661578 GT G 19273.73 PASS AC=851;AF=0.39;AFR_AF=0.52;AMR_AF=0.31;AN=2184;ASN_AF=0.37;AVGPOST=0.9823;ERATE=0.0032;EUR_AF=0.36;LDAF=0.3907;RSQ=0.9727;THETA=0.0003;VT=INDEL;set=Intersection
chr8 110105330 . A AG 435 PASS AC=893;AF=0.41;AFR_AF=0.63;AMR_AF=0.33;AN=2184;ASN_AF=0.36;AVGPOST=0.9550;ERATE=0.0070;EUR_AF=0.34;LDAF=0.4066;RSQ=0.9346;THETA=0.0005;VT=INDEL;set=variant
chr8 110106700 rs36082058 AC A 8238.66 PASS AC=223;AF=0.10;AFR_AF=0.13;AMR_AF=0.07;AN=2184;ASN_AF=0.07;AVGPOST=0.9939;ERATE=0.0004;EUR_AF=0.12;LDAF=0.1036;RSQ=0.9766;THETA=0.0003;VT=INDEL;set=Intersection
chr8 110107119 . T TA 7026.05 PASS AC=218;AF=0.10;AFR_AF=0.13;AMR_AF=0.07;AN=2184;ASN_AF=0.07;AVGPOST=0.9966;ERATE=0.0006;EUR_AF=0.12;LDAF=0.1010;RSQ=0.9859;THETA=0.0003;VT=INDEL;set=Intersection
chr8 110108673 1128681,rs35750301 GATAA G 8771.01 PASS AC=222;AF=0.10;AFR_AF=0.13;AMR_AF=0.07;AN=2184;ASN_AF=0.08;AVGPOST=0.9945;ERATE=0.0005;EUR_AF=0.12;LDAF=0.1020;RSQ=0.9774;THETA=0.0005;VT=INDEL;set=Intersection
chr8 110114056 rs35662462 GA G 6866.94 PASS AC=218;AF=0.10;AFR_AF=0.13;AMR_AF=0.07;AN=2184;ASN_AF=0.07;AVGPOST=0.9973;ERATE=0.0005;EUR_AF=0.12;LDAF=0.1003;RSQ=0.9875;THETA=0.0005;VT=INDEL;set=Intersection
chr8 110114070 . GA G 252 PASS AC=19;AF=0.01;AFR_AF=0.03;AMR_AF=0.01;AN=2184;ASN_AF=0.0035;AVGPOST=0.9968;ERATE=0.0007;LDAF=0.0090;RSQ=0.8543;THETA=0.0003;VT=INDEL;set=variant
chr8 110117987 . CATA C 19.76 PASS set=variant2
chr8 110118318 . AATAT A 222 PASS AC=17;AF=0.01;AMR_AF=0.02;AN=2184;AVGPOST=0.9952;ERATE=0.0006;EUR_AF=0.01;LDAF=0.0096;RSQ=0.8156;THETA=0.0005;VT=INDEL;set=variant
chr8 110118687 rs34199770 G GTCT 7136.95 PASS AC=66;AF=0.03;AFR_AF=0.01;AMR_AF=0.02;AN=2184;AVGPOST=0.9937;ERATE=0.0004;EUR_AF=0.07;LDAF=0.0317;RSQ=0.9279;THETA=0.0004;VT=INDEL;set=Intersection
chr8 110120839 . A AC 740.32 PASS AC=40;AF=0.02;AFR_AF=0.04;AMR_AF=0.02;AN=2184;ASN_AF=0.0035;AVGPOST=0.9720;ERATE=0.0019;EUR_AF=0.01;LDAF=0.0285;RSQ=0.6255;THETA=0.0004;VT=INDEL;set=Intersection
chr8 110125952 . AT A 8 PASS AC=36;AF=0.02;AFR_AF=0.01;AMR_AF=0.02;AN=2184;ASN_AF=0.03;AVGPOST=0.9574;ERATE=0.0088;EUR_AF=0.01;LDAF=0.0321;RSQ=0.4829;THETA=0.0002;VT=INDEL;set=variant
chr8 110127029 1227906,rs5893975 AT A 17832.88 PASS AC=911;AF=0.42;AFR_AF=0.34;AMR_AF=0.40;AN=2184;ASN_AF=0.65;AVGPOST=0.9785;ERATE=0.0025;EUR_AF=0.29;LDAF=0.4168;RSQ=0.9673;THETA=0.0001;VT=INDEL;set=Intersection
chr8 110127566 rs112898888 T TC 16971.33 PASS AC=292;AF=0.13;AFR_AF=0.33;AMR_AF=0.15;AN=2184;ASN_AF=0.10;AVGPOST=0.9951;ERATE=0.0010;EUR_AF=0.02;LDAF=0.1356;RSQ=0.9852;THETA=0.0002;VT=INDEL;set=Intersection
chr8 110132120 1274441 C CT . PASS set=variant2
chr8 110132971 . TA T 454 PASS AC=28;AF=0.01;AFR_AF=0.05;AMR_AF=0.0028;AN=2184;ASN_AF=0.0035;AVGPOST=0.9984;ERATE=0.0004;LDAF=0.0134;RSQ=0.9507;THETA=0.0003;VT=INDEL;set=variant
chr8 110133722 1193121,rs35672083 CAGGA C 29815.27 PASS AC=699;AF=0.32;AFR_AF=0.27;AMR_AF=0.30;AN=2184;ASN_AF=0.45;AVGPOST=0.9880;ERATE=0.0021;EUR_AF=0.26;LDAF=0.3223;RSQ=0.9777;THETA=0.0002;VT=INDEL;set=Intersection
chr8 110134760 . C CA 444.27 PASS AC=13;AF=0.01;AFR_AF=0.02;AN=2184;AVGPOST=0.9926;ERATE=0.0018;EUR_AF=0.0026;LDAF=0.0085;RSQ=0.6369;THETA=0.0003;VT=INDEL;set=Intersection
chr8 110138012 . GTA G 201 PASS AC=152;AF=0.07;AFR_AF=0.23;AMR_AF=0.02;AN=2184;ASN_AF=0.02;AVGPOST=0.9043;ERATE=0.0129;EUR_AF=0.03;LDAF=0.1054;RSQ=0.6186;THETA=0.0006;VT=INDEL;set=variant
chr8 110138036 . GTA G 250 PASS AC=159;AF=0.07;AFR_AF=0.07;AMR_AF=0.14;AN=2184;ASN_AF=0.11;AVGPOST=0.9757;ERATE=0.0015;EUR_AF=0.01;LDAF=0.0793;RSQ=0.8760;THETA=0.0002;VT=INDEL;set=variant
chr8 110140524 . GA G 88 PASS AC=19;AF=0.01;AFR_AF=0.04;AMR_AF=0.0028;AN=2184;AVGPOST=0.9980;ERATE=0.0005;LDAF=0.0097;RSQ=0.9180;THETA=0.0009;VT=INDEL;set=variant
chr8 110144443 . TTGAG T 367 PASS AC=20;AF=0.01;AFR_AF=0.0041;AMR_AF=0.04;AN=2184;ASN_AF=0.01;AVGPOST=0.9954;ERATE=0.0013;LDAF=0.0110;RSQ=0.8121;THETA=0.0007;VT=INDEL;set=variant
chr8 110144828 . CAGATAAT C 1801.08 PASS AC=17;AF=0.01;AFR_AF=0.03;AN=2184;AVGPOST=0.9990;ERATE=0.0003;LDAF=0.0082;RSQ=0.9469;THETA=0.0006;VT=INDEL;set=Intersection
chr8 110147656 . T TC 269 PASS AC=18;AF=0.01;AFR_AF=0.04;AN=2184;AVGPOST=0.9994;ERATE=0.0004;LDAF=0.0085;RSQ=0.9657;THETA=0.0005;VT=INDEL;set=variant
chr8 110148751 rs34297710,1127151 C CTG 61139.92 PASS AC=1104;AF=0.51;AFR_AF=0.81;AMR_AF=0.48;AN=2184;ASN_AF=0.55;AVGPOST=0.9836;ERATE=0.0003;EUR_AF=0.29;LDAF=0.5052;RSQ=0.9796;THETA=0.0005;VT=INDEL;set=Intersection
chr8 110148752 . T TGG 490 PASS AC=1099;AF=0.50;AFR_AF=0.80;AMR_AF=0.48;AN=2184;ASN_AF=0.55;AVGPOST=0.9768;ERATE=0.0010;EUR_AF=0.28;LDAF=0.5009;RSQ=0.9710;THETA=0.0005;VT=INDEL;set=variant
chr8 110148753 . G GT 161 PASS AC=1034;AF=0.47;AFR_AF=0.72;AMR_AF=0.47;AN=2184;ASN_AF=0.53;AVGPOST=0.9204;ERATE=0.0170;EUR_AF=0.27;LDAF=0.4590;RSQ=0.8924;THETA=0.0005;VT=INDEL;set=variant
chr8 110152972 . A AAGC 474 PASS AC=90;AF=0.04;AFR_AF=0.17;AMR_AF=0.0028;AN=2184;AVGPOST=0.9910;ERATE=0.0006;EUR_AF=0.0040;LDAF=0.0443;RSQ=0.9203;THETA=0.0004;VT=INDEL;set=variant
chr8 110155683 rs35101014 AT A 2563.64 PASS AC=61;AF=0.03;AFR_AF=0.11;AMR_AF=0.01;AN=2184;AVGPOST=0.9970;ERATE=0.0004;LDAF=0.0293;RSQ=0.9660;THETA=0.0003;VT=INDEL;set=Intersection
chr8 110159346 1597651,rs34432806 AT A 12911.12 PASS AC=788;AF=0.36;AFR_AF=0.41;AMR_AF=0.31;AN=2184;ASN_AF=0.46;AVGPOST=0.9879;ERATE=0.0020;EUR_AF=0.28;LDAF=0.3605;RSQ=0.9794;THETA=0.0011;VT=INDEL;set=Intersection
chr8 110159715 . A AT 158.66 PASS set=variant2
chr8 110162734 . CAT C 222.73 PASS set=variant2
chr8 110162988 . AAC A 251 PASS AC=29;AF=0.01;AFR_AF=0.0020;AMR_AF=0.02;AN=2184;AVGPOST=0.9829;ERATE=0.0006;EUR_AF=0.03;LDAF=0.0178;RSQ=0.6422;THETA=0.0004;VT=INDEL;set=variant
chr8 110164145 . TATTTATTC T 311 PASS AC=415;AF=0.19;AFR_AF=0.43;AMR_AF=0.18;AN=2184;ASN_AF=0.14;AVGPOST=0.8112;ERATE=0.0452;EUR_AF=0.08;LDAF=0.2412;RSQ=0.5769;THETA=0.0003;VT=INDEL;set=variant
chr8 110164149 . TATTC T 430 PASS AC=434;AF=0.20;AFR_AF=0.47;AMR_AF=0.21;AN=2184;ASN_AF=0.11;AVGPOST=0.8430;ERATE=0.0217;EUR_AF=0.08;LDAF=0.2349;RSQ=0.6815;THETA=0.0007;VT=INDEL;set=variant
chr8 110174424 rs113388839 TC T 2738.96 PASS AC=86;AF=0.04;AFR_AF=0.10;AMR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.9966;ERATE=0.0007;EUR_AF=0.03;LDAF=0.0402;RSQ=0.9626;THETA=0.0004;VT=INDEL;set=Intersection
chr8 110177292 . A AT 85.23 PASS set=variant2
chr8 110177965 rs35012924 A AT 9907.11 PASS AC=309;AF=0.14;AFR_AF=0.07;AMR_AF=0.21;AN=2184;ASN_AF=0.10;AVGPOST=0.9177;ERATE=0.0172;EUR_AF=0.19;LDAF=0.1642;RSQ=0.7571;THETA=0.0041;VT=INDEL;set=Intersection
chr8 110182294 . ATG A 245 PASS AC=44;AF=0.02;AFR_AF=0.09;AMR_AF=0.0028;AN=2184;AVGPOST=0.9966;ERATE=0.0006;LDAF=0.0212;RSQ=0.9307;THETA=0.0010;VT=INDEL;set=variant
chr8 110184025 . G GT 81 PASS AC=18;AF=0.01;AFR_AF=0.01;AMR_AF=0.01;AN=2184;ASN_AF=0.01;AVGPOST=0.9794;ERATE=0.0047;EUR_AF=0.01;LDAF=0.0171;RSQ=0.4794;THETA=0.0003;VT=INDEL;set=variant
chr8 110192203 . G GA 686.48 PASS AC=22;AF=0.01;AFR_AF=0.04;AN=2184;ASN_AF=0.0017;AVGPOST=0.9949;ERATE=0.0018;LDAF=0.0123;RSQ=0.8337;THETA=0.0009;VT=INDEL;set=Intersection
chr8 110194169 1142787 GTA G . PASS set=variant2
chr8 110197198 . AACTT A 309.79 PASS set=variant2
chr8 110198229 647641 GA G . PASS set=variant2
chr8 110201861 . G GT 271 PASS set=variant2
chr8 110202147 . A AC 528.04 PASS set=variant2
chr8 110203490 1078990 CAT C . PASS set=variant2
chr8 110204558 rs72441511 CCAAA C 61707.21 PASS AC=1161;AF=0.53;AFR_AF=0.30;AMR_AF=0.48;AN=2184;ASN_AF=0.63;AVGPOST=0.9847;ERATE=0.0040;EUR_AF=0.64;LDAF=0.5287;RSQ=0.9772;THETA=0.0003;VT=INDEL;set=Intersection
chr8 110206791 . G GTGCCCAACATC 9980.74 PASS AC=48;AF=0.02;AFR_AF=0.09;AMR_AF=0.01;AN=2184;AVGPOST=0.9986;ERATE=0.0003;LDAF=0.0217;RSQ=0.9723;THETA=0.0002;VT=INDEL;set=Intersection
chr8 110209216 . TTTAG T 816.15 PASS set=variant2
chr8 110209773 rs58189285 GTATAAACTCATTCT G 2429.78 PASS AC=28;AF=0.01;AFR_AF=0.05;AMR_AF=0.0028;AN=2184;AVGPOST=0.9940;ERATE=0.0004;LDAF=0.0135;RSQ=0.8381;THETA=0.0008;VT=INDEL;set=Intersection
chr8 110213818 rs112811473 G GT 20491.12 PASS AC=405;AF=0.19;AFR_AF=0.40;AMR_AF=0.11;AN=2184;ASN_AF=0.21;AVGPOST=0.9949;ERATE=0.0006;EUR_AF=0.07;LDAF=0.1853;RSQ=0.9875;THETA=0.0002;VT=INDEL;set=Intersection
chr8 110215236 . T TC 217 PASS AC=35;AF=0.02;AN=2184;ASN_AF=0.06;AVGPOST=0.9944;ERATE=0.0005;EUR_AF=0.0040;LDAF=0.0178;RSQ=0.8745;THETA=0.0007;VT=INDEL;set=variant
chr8 110215285 . CTA C 141.73 PASS set=variant2
chr8 110216060 . CAAATT C 1428.37 PASS AC=30;AF=0.01;AFR_AF=0.06;AMR_AF=0.0028;AN=2184;AVGPOST=0.9938;ERATE=0.0005;LDAF=0.0146;RSQ=0.8417;THETA=0.0017;VT=INDEL;set=Intersection
chr8 110216081 . GA G 1557.49 PASS AC=27;AF=0.01;AFR_AF=0.0041;AMR_AF=0.01;AN=2184;AVGPOST=0.9958;ERATE=0.0006;EUR_AF=0.03;LDAF=0.0139;RSQ=0.8706;THETA=0.0007;VT=INDEL;set=Intersection
chr8 110217315 . G GA 2280.52 PASS AC=33;AF=0.02;AMR_AF=0.07;AN=2184;ASN_AF=0.01;AVGPOST=0.9957;ERATE=0.0005;LDAF=0.0168;RSQ=0.8931;THETA=0.0004;VT=INDEL;set=Intersection
chr8 110218286 . A AAT 140 PASS AC=12;AF=0.01;AFR_AF=0.02;AMR_AF=0.0028;AN=2184;AVGPOST=0.9932;ERATE=0.0020;EUR_AF=0.0013;LDAF=0.0085;RSQ=0.6537;THETA=0.0003;VT=INDEL;set=variant
chr8 110219024 1156547 ATGTGTGTG A,ATG,ATGTGTGTGTG . PASS set=variant2
chr8 110220439 214372 AGT A . PASS set=variant2
chr8 110221301 1196048 A AT . PASS set=variant2
chr8 110222110 . ACT A 479.59 PASS set=variant2
chr8 110223185 . G GT 1216.41 PASS AC=32;AF=0.01;AFR_AF=0.06;AMR_AF=0.01;AN=2184;AVGPOST=0.9989;ERATE=0.0005;LDAF=0.0152;RSQ=0.9671;THETA=0.0006;VT=INDEL;set=Intersection
chr8 110223475 . G GCTAT 4171.39 PASS AC=46;AF=0.02;AFR_AF=0.09;AMR_AF=0.01;AN=2184;ASN_AF=0.0017;AVGPOST=0.9977;ERATE=0.0004;LDAF=0.0218;RSQ=0.9523;THETA=0.0006;VT=INDEL;set=Intersection
chr8 110226345 rs3070867,1208383 AAAAT A 39201.35 PASS AC=1157;AF=0.53;AFR_AF=0.29;AMR_AF=0.48;AN=2184;ASN_AF=0.62;AVGPOST=0.9789;ERATE=0.0026;EUR_AF=0.64;LDAF=0.5290;RSQ=0.9673;THETA=0.0015;VT=INDEL;set=Intersection
chr8 110227220 . TA T 6949.27 PASS AC=104;AF=0.05;AFR_AF=0.21;AMR_AF=0.01;AN=2184;AVGPOST=0.9983;ERATE=0.0004;LDAF=0.0478;RSQ=0.9860;THETA=0.0010;VT=INDEL;set=Intersection
chr8 110227880 . T TA 1091.34 PASS AC=15;AF=0.01;AN=2184;ASN_AF=0.03;AVGPOST=0.9986;ERATE=0.0004;LDAF=0.0074;RSQ=0.9274;THETA=0.0007;VT=INDEL;set=Intersection
chr8 110229788 . CA C 2041.22 PASS AC=29;AF=0.01;AFR_AF=0.05;AMR_AF=0.01;AN=2184;AVGPOST=0.9984;ERATE=0.0004;LDAF=0.0137;RSQ=0.9544;THETA=0.0008;VT=INDEL;set=Intersection
chr8 110234279 . T TA 186.97 PASS set=variant2
chr8 110234387 134382 CTATCTA C,CTATCTATATCTA . PASS set=variant2
chr8 110234427 155920 C CTA . PASS set=variant2
chr8 110241287 . CAAT C 177.50 PASS set=variant2
chr8 110243202 rs10554903 ATTTG A 391.74 PASS AC=11;AF=0.01;AFR_AF=0.02;AN=2184;AVGPOST=0.9995;ERATE=0.0003;LDAF=0.0051;RSQ=0.9585;THETA=0.0008;VT=INDEL;set=Intersection
chr8 110243269 . CTGTT C 305 PASS AC=11;AF=0.01;AFR_AF=0.01;AMR_AF=0.02;AN=2184;AVGPOST=0.9995;ERATE=0.0004;EUR_AF=0.0013;LDAF=0.0053;RSQ=0.9543;THETA=0.0003;VT=INDEL;set=variant
chr8 110244271 . T TA 565.50 PASS set=variant2
chr8 110244857 . ATAGT A 213.25 PASS set=variant2
chr8 110246344 . C CT 362.86 PASS set=variant2
chr8 110247756 rs35903315 TTAGA T 23042.33 PASS AC=282;AF=0.13;AFR_AF=0.02;AMR_AF=0.22;AN=2184;ASN_AF=0.09;AVGPOST=0.9858;ERATE=0.0005;EUR_AF=0.18;LDAF=0.1312;RSQ=0.9541;THETA=0.0006;VT=INDEL;set=Intersection
chr8 110248217 . CATCATATATAT C 645 PASS AC=143;AF=0.07;AFR_AF=0.0041;AMR_AF=0.09;AN=2184;AVGPOST=0.9771;ERATE=0.0010;EUR_AF=0.14;LDAF=0.0702;RSQ=0.8636;THETA=0.0014;VT=INDEL;set=variant
chr8 110249494 1613673 G GA . PASS set=variant2
chr8 110252848 . T TATATGTTG 198 PASS AC=22;AF=0.01;AMR_AF=0.01;AN=2184;AVGPOST=0.9949;ERATE=0.0004;EUR_AF=0.02;LDAF=0.0108;RSQ=0.8180;THETA=0.0010;VT=INDEL;set=variant
chr8 110252862 . C CAT 381 PASS AC=1613;AF=0.74;AFR_AF=0.94;AMR_AF=0.59;AN=2184;ASN_AF=0.78;AVGPOST=0.9384;ERATE=0.0018;EUR_AF=0.64;LDAF=0.7279;RSQ=0.8989;THETA=0.0008;VT=INDEL;set=variant
chr8 110252863 1286860 A ATAT . PASS set=variant2
chr8 110252865 . A ATT 470 PASS AC=1561;AF=0.71;AFR_AF=0.88;AMR_AF=0.57;AN=2184;ASN_AF=0.77;AVGPOST=0.9095;ERATE=0.0094;EUR_AF=0.63;LDAF=0.7008;RSQ=0.8541;THETA=0.0010;VT=INDEL;set=variant
chr8 110257510 . AAT A 1226.81 PASS AC=23;AF=0.01;AFR_AF=0.05;AN=2184;AVGPOST=0.9980;ERATE=0.0004;LDAF=0.0107;RSQ=0.9191;THETA=0.0004;VT=INDEL;set=Intersection
chr8 110258735 . TTAA T 334 PASS AC=26;AF=0.01;AMR_AF=0.01;AN=2184;AVGPOST=0.9974;ERATE=0.0003;EUR_AF=0.03;LDAF=0.0125;RSQ=0.9170;THETA=0.0008;VT=INDEL;set=variant
chr8 110263236 1286846,rs3044032 T TTTCC 72090.63 PASS AC=1610;AF=0.74;AFR_AF=0.88;AMR_AF=0.59;AN=2184;ASN_AF=0.82;AVGPOST=0.9869;ERATE=0.0011;EUR_AF=0.65;LDAF=0.7353;RSQ=0.9750;THETA=0.0007;VT=INDEL;set=Intersection
chr8 110264233 rs67360064 TTATATC T 62997.03 PASS AC=1111;AF=0.51;AFR_AF=0.32;AMR_AF=0.46;AN=2184;ASN_AF=0.60;AVGPOST=0.9906;ERATE=0.0009;EUR_AF=0.59;LDAF=0.5082;RSQ=0.9854;THETA=0.0004;VT=INDEL;set=Intersection
chr8 110266836 rs3044031 G GACCA 21807.13 PASS AC=242;AF=0.11;AFR_AF=0.03;AMR_AF=0.19;AN=2184;ASN_AF=0.09;AVGPOST=0.9864;ERATE=0.0006;EUR_AF=0.14;LDAF=0.1097;RSQ=0.9482;THETA=0.0008;VT=INDEL;set=Intersection
chr8 110266956 . TC T 172 PASS AC=14;AF=0.01;AN=2184;ASN_AF=0.02;AVGPOST=0.9987;ERATE=0.0003;LDAF=0.0067;RSQ=0.9215;THETA=0.0006;VT=INDEL;set=variant
chr8 110269140 . TATAAACC T 460 PASS AC=28;AF=0.01;AFR_AF=0.05;AMR_AF=0.0028;AN=2184;AVGPOST=0.9981;ERATE=0.0003;LDAF=0.0133;RSQ=0.9449;THETA=0.0004;VT=INDEL;set=variant
chr8 110269149 . AAAAACCTT A 478 PASS AC=28;AF=0.01;AFR_AF=0.05;AMR_AF=0.0028;AN=2184;AVGPOST=0.9980;ERATE=0.0004;LDAF=0.0133;RSQ=0.9440;THETA=0.0007;VT=INDEL;set=variant
chr8 110272074 . TA T 2317.84 PASS AC=62;AF=0.03;AFR_AF=0.12;AMR_AF=0.01;AN=2184;AVGPOST=0.9924;ERATE=0.0005;EUR_AF=0.0013;LDAF=0.0301;RSQ=0.9082;THETA=0.0005;VT=INDEL;set=Intersection
chr8 110277147 2750650 AGT A . PASS set=variant2
jamesdalg commented
Looks like this is fixed.
download the latest chains here: https://hgwdev.gi.ucsc.edu/~markd/t2t/CHM13-fixed-chains/
diekhans commented
this should still be fixed in S3 .. sorry for wasting your time.!