I need to query a set of chromosomal positions towards a couple of BAM files, and I am using samtools mpileup for this. Following is my command line,
samtools mpileup -L 1000000 -u -A -B -d 100000 -Q 0 -t DP -t AD -t ADF -t ADR -f GRCh37.fa --positions mybed.bed sample1.bam sample2.bam sample3.bam sample3.bam sample4.bam ... sampleN.bam >test.vcf
I could find the positions in my bed file within that sample.bam files when I look into IGV for certain samples but the above command line is not able to identify those positions.
Any help would be great . My aim is to get the read depth of the chromosomal position defined in my bed file from BAM files