Entering edit mode
23 months ago
esimonova.me ▴ 20
Our lab sequenced NA12763 sample in order to validate a bioinformatics pipeline for the analysis of data. I am not sure where can I find a validation vcf file to compare a generated vcf with a sequenced one (via hap.py tool)?
I just found that the sample was sequenced in 1000G project but vcf doesn't seem to be the one I need, I am still junior in bioinformatics but it is the first time I see ALT column described in the following way:
1 1 . N **<CGA_NOCALL**> . . END=10000;NS=1;AN=0 GT:PS ./.:. 1 10001 . T **<CGA_CNVWIN>** . . NS=1;CGA_WINEND=12000 1 10001 . T **<CGA_NOCALL>**
It is written that snv and indel file even though I think it is CGA array CNV data.