Varscan Mpileup2Snp Output Missing Varfreq Values

Question

[GPR]

Hello, I am running an SNP analysis and have two questions about the output.

My command-line is the following: samtools mpileup -f genome.fa left-reads.bam right reads.bam | --min-avg-qual 25 --p-value 0.01 --min-freq-for-hom 0.95 --output-vcf 1 --min-var-freq 0.2 -> output.vcf &

Question 1: the output.vcf is missing the VarFreq information. Can somebody tell me what am I missing here in order to get VarFreq values?

Question 2: my output contains info for two samples. Does this reflect the fact that my input contains 2 bam files? Or am I missing something about the meaning of Sample 1 and Sample 2? Thanks, G.

Answer 1

[dankoboldt]

Hello, and thanks for your questions.

1.) In the latest version of VarScan, the VAF should be provided in the FREQ column of the sample's genotype when you output to VCF. You can also get it by using VarScan's native output. If you don't see this, please let me know which version of VarScan you're using.

2.) Yes, it's because you're providing two BAM files to mpileup, which it (and VarScan) treat like two different samples. If you want a single result, merge the BAM files before mpileup.