Using build_background for gnomAD v3

[j2moreno]

Hi,

I am having trouble creating a background using gnomAD v3.

https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz

Command ran:

build_background -i gnomad.genomes.r3.0.sites.vcf.bgz -b 1 -v CSQ,4,6,1,15 -o test.out

I receive the error:

#chr    start   ref     var     transcript      hemi_score      het_score       hom_score       nhemi   nhet    nhom    hemi_nocall     het_nocall      hom_nocall      coding_ind
VCF FORMAT PROBLEM:      vcf line has fewer than 10 columns, will skip: chr1:10031, C, AC=0;AN=53780;AF=0.00000e+00;lcr;variant_type=snv;n_alt_alleles=1;ReadPosRankSum=-1.38000e+00;MQRankSum=-5.72000e-01;RAW_MQ=6.39630e+04;DP=26;MQ_DP=52;VarDP=26;MQ=3.50722e+01;QD=2.96154e+00;FS=5.09715e+00;SB=21,6,3,3;InbreedingCoeff=-1.72592e-05;AS_VQSLOD=-9.41040e+00;NEGATIVE_TRAIN_SITE;culprit=AS_MQ;SOR=9.60000e-02;AC_asj_female=0;AN_asj_female=776;AF_asj_female=0.00000e+00;nhomalt_asj_female=0;AC_eas_female=0;AN_eas_female=558;AF_eas_female=0.00000e+00;nhomalt_eas_female=0;AC_afr_male=0;AN_afr_male=6700;AF_afr_male=0.00000e+00;nhomalt_afr_male=0;AC_female=0;AN_female=27974;AF_female=0.00000e+00;nhomalt_female=0;AC_fin_male=0;AN_fin_male=3278;AF_fin_male=0.00000e+00;nhomalt_fin_male=0;AC_oth_female=0;AN_oth_female=430;AF_oth_female=0.00000e+00;nhomalt_oth_female=0;AC_ami=0;AN_ami=350;AF_ami=0.00000e+00;nhomalt_ami=0;AC_oth=0;AN_oth=802;AF_oth=0.00000e+00;nhomalt_oth=0;AC_male=0;AN_male=25806;AF_male=0.00000e+00;nhomalt_male=0;AC_ami_female=0;AN_ami_female=150;AF_ami_female=0.00000e+00;nhomalt_ami_female=0;AC_afr=0;AN_afr=14854;AF_afr=0.00000e+00;nhomalt_afr=0;AC_eas_male=0;AN_eas_male=612;AF_eas_male=0.00000e+00;nhomalt_eas_male=0;AC_sas=0;AN_sas=606;AF_sas=0.00000e+00;nhomalt_sas=0;AC_nfe_female=0;AN_nfe_female=14256;AF_nfe_female=0.00000e+00;nhomalt_nfe_female=0;AC_asj_male=0;AN_asj_male=720;AF_asj_male=0.00000e+00;nhomalt_asj_male=0;AC_raw=2;AN_raw=115882;AF_raw=1.72589e-05;nhomalt_raw=0;AC_oth_male=0;AN_oth_male=372;AF_oth_male=0.00000e+00;nhomalt_oth_male=0;AC_nfe_male=0;AN_nfe_male=10036;AF_nfe_male=0.00000e+00;nhomalt_nfe_male=0;AC_asj=0;AN_asj=1496;AF_asj=0.00000e+00;nhomalt_asj=0;AC_amr_male=0;AN_amr_male=3392;AF_amr_male=0.00000e+00;nhomalt_amr_male=0;nhomalt=0;AC_amr_female=0;AN_amr_female=2454;AF_amr_female=0.00000e+00;nhomalt_amr_female=0;AC_sas_female=0;AN_sas_female=110;AF_sas_female=0.00000e+00;nhomalt_sas_female=0;AC_fin=0;AN_fin=4364;AF_fin=0.00000e+00;nhomalt_fin=0;AC_afr_female=0;AN_afr_female=8154;AF_afr_female=0.00000e+00;nhomalt_afr_female=0;AC_sas_male=0;AN_sas_male=496;AF_sas_male=0.00000e+00;nhomalt_sas_male=0;AC_amr=0;AN_amr=5846;AF_amr=0.00000e+00;nhomalt_amr=0;AC_nfe=0;AN_nfe=24292;AF_nfe=0.00000e+00;nhomalt_nfe=0;AC_eas=0;AN_eas=1170;AF_eas=0.00000e+00;nhomalt_eas=0;AC_ami_male=0;AN_ami_male=200;AF_ami_male=0.00000e+00;nhomalt_ami_male=0;AC_fin_female=0;AN_fin_female=1086;AF_fin_female=0.00000e+00;nhomalt_fin_female=0;faf95_afr=0.00000e+00;faf99_afr=0.00000e+00;faf95_sas=0.00000e+00;faf99_sas=0.00000e+00;faf95_adj=0.00000e+00;faf99_adj=0.00000e+00;faf95_amr=0.00000e+00;faf99_amr=0.00000e+00;faf95_nfe=0.00000e+00;faf99_nfe=0.00000e+00;faf95_eas=0.00000e+00;faf99_eas=0.00000e+00;vep=C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||
Segmentation fault (core dumped)

Is build background not compatible with this new gnomAD version?