Validation of Bioinformatics pipeline with NA12763
Entering edit mode
23 months ago ▴ 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 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. • 343 views

Login before adding your answer.

Traffic: 1310 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6