Question: bam-readcount error bam_header_read
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fangqiong.ling • 0 wrote:
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
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modified 4 months ago
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Chris Miller ♦ 18k
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written
4 months ago by
fangqiong.ling • 0
Have you verified that your bam looks legit with
samtools view sample1_sorted.bam | less