VCF files

Question

[Sanazarghami4444]

Hello, I run this code for produce VCF files of samples that i work on it :

java -jar picard.jar MarkDuplicates \
  INPUT=/home/zr/SRR3229050/SRR3229050_sorted.bam \
  OUTPUT=SRR3229050_sorted.rmdup.bam \
  METRICS_FILE=SRR3229050.dedup.Metrics \
  VALIDATION_STRINGENCY=LENIENT \
  MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=50

I want to sure this code is true? And I want to know how can I check that my vcf files that produced are true and valid?

[Pierre Lindenbaum]

this code is part of a larger workflow that map the fastq to bam file before calling the VCF. But this code alone is unrelated to the VCF format.

Answer 1

[Kevin Blighe]

Please follow the workflow for Germline short variant discovery (SNPs + Indels):

https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels

Kevin