I use samtools for calling SNP. I running many samples with the same code. Most of samples is normal. I met some error files from a few samples. Could you tell me what it happened?
My code is samtools mpileup -u -g -f /depot/tmengist/data/ref/Sb_ref/Sb21b.fa SSSS.realn.bam | bcftools call -mv > SSSS.samtools.raw.vcf
The error files is
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bam_plp_destroy] memory leak: 353. Continue anyway.