Example data output incorrect?
kc199 opened this issue · 8 comments
kc199 commented
Hi, I had a question about the correct output for the test data included in the Github. I downloaded test.cram from mutserve/test-data/mtdna/cram/input/, and also downloaded the latest version of mutserve, v2.0.0-rc12. I then ran the tool as follows:
./mutserve call test.cram --reference rCRS.fasta --output TEST.vcf.gz
The tool completed but in the resulting variant file, I only have 51 variants, several of which say "STRAND_BIAS". However, in the output file you have posted to the github under mutserve/test-data/mtdna/cram/output/variants.txt, there are 85 variants, none of which say "STRAND_BIAS" e.g. all are "PASS".
I was wondering why my output does not match yours; perhaps I'm running mutserve incorrectly? Thanks!
haansi commented
Dear kc199,
You should run both files test.cram and test1.cram to get the correct result, as the output file contains the variants of both samples.
kc199 commented
Dear Hansi,
Thank you for your response and the clarification. I tried running both
test.cram and test1.cram, and have attached the results. My results almost
match the variants you have posted on the Github, but still not exactly.
For example, we can see that variant G/A at position 15355, and variant A/G
at position 5894 in your file are not present in my results. Similarly, in
my results there is a variant T/C at position 310, not present in your
file.
Could you advise if I have made a mistake? Thank you!
On Wed, Nov 17, 2021 at 9:04 AM Hansi Weißensteiner < ***@***.***> wrote:
Dear kc199,
You should run both files test.cram and test1.cram to get the correct
result, as the output file contains the variants of both samples.
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ID Filter Pos Ref Variant VariantLevel MajorBase MajorLevel MinorBase MinorLevel Coverage CoverageFWD CoverageREV Type
test.cram PASS 73 A G 0.999 G 0 - 0 1143 579 564 1
test.cram PASS 263 A G 0.999 G 0 - 0 1014 495 519 1
test.cram PASS 310 T C 0.858 C 0.858 T 0.142 808 334 474 2
test.cram PASS 417 G A 0.997 A 0 - 0 1204 628 576 1
test.cram PASS 489 T C 0.998 C 0 - 0 1117 612 505 1
test.cram PASS 513 G A 0.045 G 0.954 A 0.045 1076 572 504 2
test.cram PASS 750 A G 1 G 0 - 0 1214 619 595 1
test.cram PASS 1438 A G 0.999 G 0 - 0 1471 811 660 1
test.cram PASS 2089 T C 0.064 T 0.936 C 0.064 1599 815 784 2
test.cram PASS 3107 N T 0.632 T 0.632 C 0.342 38 18 20 2
test.cram PASS 3483 G A 0.984 A 0 - 0 885 602 283 1
test.cram PASS 4386 T C 0.041 T 0.959 C 0.041 883 468 415 2
test.cram PASS 4769 A G 1 G 0 - 0 878 570 308 1
test.cram PASS 7028 C T 1 T 0 - 0 968 528 440 1
test.cram PASS 8010 T C 0.146 T 0.854 C 0.146 1301 621 680 2
test.cram PASS 8149 A G 0.994 G 0 - 0 1418 704 714 1
test.cram PASS 8188 A G 0.994 G 0 - 0 1432 645 787 1
test.cram PASS 8701 A G 0.997 G 0 - 0 1719 719 1000 1
test.cram PASS 8731 T C 0.084 T 0.915 C 0.084 1620 747 873 2
test.cram PASS 8860 A G 1 G 0 - 0 784 285 499 1
test.cram PASS 9438 G A 0.996 A 0 - 0 1638 730 908 1
test.cram PASS 9540 T C 0.999 C 0 - 0 1500 876 624 1
test.cram PASS 9949 T C 0.044 T 0.956 C 0.044 1598 763 835 2
test.cram PASS 10295 A G 0.997 G 0 - 0 1257 853 404 1
test.cram PASS 10398 A G 0.997 G 0 - 0 1543 731 812 1
test.cram PASS 10400 C T 0.997 T 0 - 0 1569 753 816 1
test.cram PASS 10873 T C 0.997 C 0 - 0 1753 867 886 1
test.cram PASS 11719 G A 1 A 0 - 0 1453 708 745 1
test.cram PASS 11899 T C 0.992 C 0 - 0 1426 736 690 1
test.cram PASS 12279 A G 0.994 G 0 - 0 1619 761 858 1
test.cram PASS 12705 C T 0.995 T 0 - 0 1519 781 738 1
test.cram PASS 14766 C T 0.999 T 0 - 0 1726 846 880 1
test.cram PASS 14783 T C 0.996 C 0 - 0 1661 851 810 1
test.cram PASS 15025 C T 0.996 T 0 - 0 1470 702 768 1
test.cram PASS 15043 G A 0.997 A 0 - 0 1475 691 784 1
test.cram PASS 15229 T C 0.997 C 0 - 0 1438 767 671 1
test.cram PASS 15301 G A 0.997 A 0 - 0 1206 684 522 1
test.cram PASS 15326 A G 1 G 0 - 0 1384 749 635 1
test.cram PASS 16126 T C 0.999 C 0 - 0 1482 754 728 1
test.cram PASS 16189 T C 0.999 C 0 - 0 1147 510 637 1
test.cram PASS 16209 T C 0.993 C 0 - 0 1038 334 704 1
test.cram PASS 16220 A G 0.995 G 0 - 0 1032 354 678 1
test.cram PASS 16223 C T 0.997 T 0 - 0 1111 446 665 1
test.cram PASS 16270 C G 0.997 G 0 - 0 1312 508 804 1
test.cram PASS 16311 T C 0.998 C 0 - 0 1310 580 730 1
test.cram PASS 16519 T C 0.999 C 0 - 0 1101 552 549 1
test1.cram PASS 73 A G 1 G 0 - 0 170 72 98 1
test1.cram PASS 152 T C 0.98 C 0.98 T 0.02 253 91 162 2
test1.cram PASS 182 C T 0.024 C 0.972 T 0.024 248 100 148 2
test1.cram PASS 195 T C 0.029 T 0.971 C 0.029 243 110 133 2
test1.cram PASS 228 G A 0.962 A 0.962 G 0.038 211 108 103 2
test1.cram PASS 263 A G 1 G 0 - 0 177 94 83 1
test1.cram PASS 310 T C 0.898 C 0.898 T 0.102 108 38 70 2
test1.cram PASS 750 A G 1 G 0 - 0 240 126 114 1
test1.cram PASS 1438 A G 0.993 G 0 - 0 302 151 151 1
test1.cram PASS 2706 A G 1 G 0 - 0 235 68 167 1
test1.cram PASS 3308 T C 0.016 T 0.984 C 0.016 320 145 175 2
test1.cram PASS 4769 A G 1 G 0 - 0 143 101 42 1
test1.cram PASS 7028 C T 0.995 T 0 - 0 188 83 105 1
test1.cram PASS 7897 G A 0.984 A 0 - 0 308 131 177 1
test1.cram PASS 8701 A G 0.018 A 0.982 G 0.018 326 154 172 2
test1.cram PASS 8860 A G 0.994 G 0 - 0 178 31 147 1
test1.cram PASS 9540 T C 0.033 T 0.967 C 0.033 299 171 128 2
test1.cram PASS 10398 A G 0.03 A 0.97 G 0.03 301 156 145 2
test1.cram PASS 10873 T C 0.027 T 0.973 C 0.027 293 157 136 2
test1.cram PASS 11075 T C 0.973 C 0 - 0 291 154 137 1
test1.cram PASS 11719 G A 1 A 0 - 0 316 154 162 1
test1.cram PASS 12133 C T 0.967 T 0.967 C 0.033 304 146 158 2
test1.cram PASS 12285 T C 0.972 C 0 - 0 290 147 143 1
test1.cram PASS 12684 G A 0.02 G 0.98 A 0.02 303 153 150 2
test1.cram PASS 12705 C T 0.052 C 0.948 T 0.052 328 160 168 2
test1.cram PASS 13105 A G 0.024 A 0.976 G 0.024 290 134 156 2
test1.cram PASS 13650 C T 0.037 C 0.963 T 0.037 273 137 136 2
test1.cram PASS 14058 C T 0.968 T 0.968 C 0.032 315 146 169 2
test1.cram PASS 14766 C T 1 T 0 - 0 313 150 163 1
test1.cram PASS 15067 T C 0.964 C 0 - 0 279 152 127 1
test1.cram PASS 15326 A G 1 G 0 - 0 261 146 115 1
test1.cram PASS 16129 G A 0.981 A 0.981 G 0.019 308 172 136 2
test1.cram PASS 16213 G A 0.974 A 0.974 G 0.026 267 142 125 2
test1.cram PASS 16278 C T 0.02 C 0.977 T 0.02 304 118 186 2
test1.cram PASS 16311 T C 0.016 T 0.98 C 0.016 304 127 177 2
test1.cram PASS 16320 C T 0.949 T 0.949 C 0.051 293 132 161 2
test1.cram PASS 16362 T C 0.974 C 0.974 T 0.026 302 174 128 2
test1.cram PASS 16368 T C 0.949 C 0.949 T 0.051 316 180 136 2
test1.cram PASS 16519 T C 0.982 C 0 - 0 228 91 137 1
kc199 commented
Dear Hansi,
I wanted to follow up on my last message. Could you advise how to obtain
the correct output posted to the Github? Thank you!
On Wed, Nov 17, 2021 at 11:03 PM Chirag Krishna ***@***.***>
wrote:
… Dear Hansi,
Thank you for your response and the clarification. I tried running both
test.cram and test1.cram, and have attached the results. My results almost
match the variants you have posted on the Github, but still not exactly.
For example, we can see that variant G/A at position 15355, and variant A/G
at position 5894 in your file are not present in my results. Similarly, in
my results there is a variant T/C at position 310, not present in your
file.
Could you advise if I have made a mistake? Thank you!
On Wed, Nov 17, 2021 at 9:04 AM Hansi Weißensteiner <
***@***.***> wrote:
> Dear kc199,
>
> You should run both files test.cram and test1.cram to get the correct
> result, as the output file contains the variants of both samples.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#44 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AUEDBX4W2MEYN54BC2JEAGDUMOY5FANCNFSM5IAIXPWQ>
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>
seppinho commented
hi,
will double check and let you know
sebastian
kc199 commented
Thank you, Sebastian.
…On Tue, Nov 30, 2021 at 12:27 PM Sebastian Schoenherr < ***@***.***> wrote:
hi,
will double check and let you know
sebastian
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kc199 commented
Hi Sebastian, just following up on this- any luck with the example output?
On Tue, Nov 30, 2021 at 12:29 PM Chirag Krishna ***@***.***>
wrote:
… Thank you, Sebastian.
On Tue, Nov 30, 2021 at 12:27 PM Sebastian Schoenherr <
***@***.***> wrote:
> hi,
> will double check and let you know
> sebastian
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
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seppinho commented
Hi,
When executing both files and grep for PASS the output is identical to the output on github (85 variants). The txt also includes now a filter column including variants which are not passed. But if you grep for PASS you should get the same output. Hope this helps!
./mutserve call test*.cram --reference rCRS.fasta --output test.txt
cat test.txt | grep PASS | wc -l
seppinho commented
Fyi, the input are both test input files, test.cram and test1.cram.