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?