Hello.
I have a BAM file that I need to filter and then update the header for.
These are my commands:
The first 3 commands execute without any problems.
Using
I can see that the new BAM file does indeed contain the correct header.
However every time I run the sorting command I get the error message:
The samp1234.clean.reheaded.bam file seems to be fine in every regard. I can't seem to find a fault with it .
Performing the reheading step in place doesn't seem to help nor does the -P option
Does anyone have a suggestion of what I'm doing wrong?
In case it helps I'm using samtools version 1.4-5-g692e058 (using htslib 1.4-5-g10bc1a7)
Thanks in advance for any and all help.
I have a BAM file that I need to filter and then update the header for.
These are my commands:
Code:
samtools view -@ 32 -h -b -f 2 -T /data/hs37d5.fa \ -o samp1234.clean.bam \ bam.files/samp1234.bam \ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y MT samtools view -H samp1234.clean.bam | \ grep -v -e 'SN:GL' -e 'SN:NC' -e 'SN:hs37d5' \ > samp1234.corrected.sam samtools reheader samp1234.corrected.sam \ samp1234.clean.bam > samp1234.clean.reheaded.bam samtools sort -@ 32 \ -o samp1234.clean.reheaded.sorted.bam \ samp1234.clean.reheaded.bam
The first 3 commands execute without any problems.
Using
Code:
samtools view -h samp1234.clean.reheaded.bam | less -S
However every time I run the sorting command I get the error message:
Code:
samtools sort: truncated file. Aborting
Performing the reheading step in place doesn't seem to help nor does the -P option
Does anyone have a suggestion of what I'm doing wrong?
In case it helps I'm using samtools version 1.4-5-g692e058 (using htslib 1.4-5-g10bc1a7)
Thanks in advance for any and all help.
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