Question: bam-readcount error bam_header_read
gravatar for fangqiong.ling
13 months ago by
fangqiong.ling0 wrote:


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

ADD COMMENTlink modified 13 months ago by Chris Miller19k • written 13 months ago by fangqiong.ling0

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

ADD REPLYlink written 13 months ago by Chris Miller19k
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