Entering edit mode
16 days ago
Anitha
•
0
For 3 paired end sample of tumor, normal and blood. I need to do somatic and germline variant calling. I did mapping, sorting, addorreplacereadgroup, markduplicates, created the recal.table with the --known-sites dbSNP.vf, applybqsr. After this what is the step to proceed for calling variants for both germline and somatic. My question is in this is for germline variant calling haplotypecaller is used but with this what I need to generate .vcf or .g.vcf file? And for somatic mutation which bam I need to use llike tumor, normal or blood. For germline do I need to generate vcf or gvcf for each 3 samples?
