bam-readcount error bam_header_read

Question

[fangqiong.ling]

Hey!

I'm running bam-headcount to get allele frequency from mapped reads. I got the following error messages:

Minimum mapping quality is set to 0 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). Segmentation fault: 11

My bam file was created with

samtools view -hbS sample1.sam > sample1.bam
samtools sort sample1.bam -o sample1_sorted

thus output has been specified as BAM and with header.

Any idea what might have gone wrong?

Thanks! Fangqiong

[Chris Miller]

Have you verified that your bam looks legit with samtools view sample1_sorted.bam | less