I am using samtools mpileup on multi bam files to genrate vcf file. mpileup seems to be working with only 6 bam files but not on more than 6 files. If I enter more than 6 files, samtools finishes without error in approx 2min and the vcf file generated is empty except for the header. I have used this command line in the past to call vcf from as many as 10 bam files. Now I need to increase it to 58 bam files. But it is failing if I include more than 6 bam files.
the command line I am using
/home/sb47/Programs/samtools-1.3.1/samtools mpileup -uv \ -l /scratch/sb47cp/global_seq_Rnorvegicus/858_positions \ -f /scratch/sb47cp/Ref_5_71/Rattus_norvegicus.Rnor_5.0.71.dna_sm.toplevel.fa \ -b bams.list | /home/sb47/Programs/samtools-1.3.1/bcftools-1.3.1/bcftools call -c \ > /scratch/sb47cp/FranceIce_858loci.vcf
bams.list is the list of bam files.
Can anyone please help me with this? I unable to figure out why it is not working.