sridnona
commented
4 years ago hi @lagzxadr , Apologies for delayed response.
As referenced in previous issue, this is WIP will keep you posted.
One work around is to to use vep to annotate your vcf and use this to convert it to a table format, https://vatools.readthedocs.io/en/latest/vep_annotation_reporter.html
Thanks Sid
Dear Sid,
I am trying to use cb_sniffer for my 10x 3' Gene expression data and I tired a vcf generated from gatk haplotypecaller as well as a downloaded ClinVar vcf fromNCBI (https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/). But unfortunately, I got "DEBUG Insufficient columns fields please check variant file" for both.
I looked at my vcf file (the gatk generated one). It is v4.2 and looks a bit different from your REAME.md example with starting from "##fileformat=VCFv4.2" ... to "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AML1_Internal" and ... "chrUn_KI270330v1 1164 . A T 69.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.70;ReadPosRankSum=-0.135;SOR=0.368 GT:AD:DP:GQ:PL 0/1:5,3:8:77:77,0,146" (end) . The format looks more like (https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/variant-identification-and-analysis-0). I am wondering how can I make the vcf file work in cb_sniffer. Can I get a set of vcf file for GRCh38 from you? Or would you give some suggestions to use cb_sniffer properly?
Thank you very much!