Dear all,
I got the error "[GangSTR-2.5.0] ERROR: Error extracting read length" when I run GangSTR. I try to found solution but noway.
First, I make sure the reference matches what my bam file is aligned to (version and annotation, i.e., chrX vs X).
Then I only remain all the reads with length=150bp using the command:
"samtools view -h my.bam | awk 'length($10) == 150 || $1~/^@/' | samtools view -b -@ 2 -o my.cl.bam -"
Finally, I still got the error: "Error extracting read length"
What should I do? I'm looking forward to your reply.
Best wishes.
Dear all,
I got the error "[GangSTR-2.5.0] ERROR: Error extracting read length" when I run GangSTR. I try to found solution but noway.
First, I make sure the reference matches what my bam file is aligned to (version and annotation, i.e., chrX vs X).
Then I only remain all the reads with length=150bp using the command:
"samtools view -h my.bam | awk 'length($10) == 150 || $1~/^@/' | samtools view -b -@ 2 -o my.cl.bam -"
Finally, I still got the error: "Error extracting read length"
What should I do? I'm looking forward to your reply.
Best wishes.