Varscan2.3 to generate vcf files. I understand that we need to convert the BAM files to mpileup format first and then give it as an input. But I keep getting an error.
The command I used:
samtools mpileup -f ~/refs/human_g1k_v37.fasta file.bam | java -jar /varscan/VarScan.v2.3 mpileup2snp --output-vcf > raw.vcf
I get the following error:
Error: Invalid format for pileup at line 12 1 11829 A 0
There was a thread already (Varscan Error On Mpileup Input), but that didn't help me. Does anyone know how to resolve this?