VCF error

Dear GATK,

We run two batches of targeted sequencing capture. The first batch consisted of 24 samples and the size of the target region is 770 kbp on chromsome 3. The second batch consisted of 72 samples and the size of the target region is 780 kbp on chromosome 8. Variant discovery and genotype calling for each batch were performed separately. We used the recommended Best Practices workflow except for the VQSR step; due to our samples size and also target size, we applied hard filter instead.

I tried to run snpEff using the vcf outputs and encountered an error. The error was due to the presence of '*" in the ALT column (please find the following example).

CHROM POS ID REF ALT QUAL FILTER

3 36839160 rs200561114 A T,*
3 36959990 rs56667179 GA G,* 6179.18 PASS
3 37003227 . T A,* 345.12 PASS

Do you know the likely cause and solution of this error?

Thank you for your help and I look forward to hearing from you.

Yours sincerely,

Michael

Answers

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