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Sam file header and truncated file

I posted this on the samtools groups with no luck, so hopefully here i get better luck

I'm changing part of the header in a number of bam files. however, after I do that, the resulting bam file is truncated....

I used the following code borrowed/adapted from here

samtools view -H file.bam | grep  'SN:X\|^@RG\|^@PG\|^@HD' | samtools reheader - file.bam > bam_final/new_name.bam

and 

samtools view -h bam_final/new_name.bam

gives me

[main_samview] truncated file.

right after the new header.... any suggestions?

sam samtools header
• 4,913 views • link
updated by Volkan Sevim • Volkan Sevim • written by TriS TriS

You are only doing a grep for the pattern but are not changing anything? Is that what you meant to do? The thread you linked uses sed to make changes and then writing them out using samtools reheader.

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written by GenoMax GenoMax

yes, I wanted to grep out only the X chr and the three headers indicated. I did use samtools reheader indeed

• 0 views • link
written by TriS TriS

Not sure I understand what you want to do. Leave only the headers for X and remove others? If you only run the command up to the grep part, do you get what you expected to see?

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written by GenoMax GenoMax

that's correct and I do get the header I expect to see.

• 0 views • link
written by TriS TriS

I just tried your command on a file (selecting for just chrX) with samtools v. 1.3.1 and was able to re-header the file without an error. What version of samtools are you using?

• 0 views • link
written by GenoMax GenoMax

Version: 1.3-27-g6994f30 (using htslib 1.3-51-g55ff37c)

hmmm...I need to see if we have an earlier version on the server... so your bam file was not truncated, correct?

• 0 views • link
written by TriS TriS

I do not get any error with samtools view -H and the size looks about the same after re-header.

• 0 views • link
written by GenoMax GenoMax

have you tried to look at the first few lines? below the header like 

samtools view -h mybam.bam | head

i still get the truncated file error

• 0 views • link
written by TriS TriS

1 answer

Bam format references to read groups by their respective number in the header. Therefore when you remove some read groups from the header, samtools gets confused. You should convert your bam to sam first, update the header, then convert back to sam. Just take all lines that contain your chromosome name (header+reads) along with the @HD and @PG lines in the header, then convert to sam:

samtools view $bamfile $chromosome | \
     grep -P "@HD|@PG|$chromosome" | \
     samtools view -Shb > $chromosome.bam
• 1 views • link
written by Volkan Sevim • Volkan Sevim

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