How to combine two .sam files?

Question

[luzglongoria]

Hi there,

I just wonder if I can combine two .sam files. I am not sure if the ‘cat’ command would work in this case. I would like the final file to be a .sam file as well.

Thank you so much.

[Pierre Lindenbaum]

samtools merge or picard https://broadinstitute.github.io/picard/command-line-overview.html#MergeSamFiles

[WouterDeCoster]

Why work on sam files and not bam?

[grant.hovhannisyan]

Or maybe even combine fastq files with cat if you have them?

[WouterDeCoster]

It can be more efficient to run alignments in parallel and merge afterwards.

[luzglongoria]

I have converted SAM files into BAM files

samtools view -bS -o /PATH/file1.sam > file1.bam
samtools view -bS -o /PATH/file2.sam > file2.bam

Now I wan to combine these 2 files with this command:

samtools merge out.bam file1.bam file2.bam

But I got this error message

[W::bam_merge_core2] No @HD tag found.
[W::sam_read1] parse error at line 2

It's something wrong with my BAM files?

[Pierre Lindenbaum]

No @HD tag found. It's something wrong with my BAM files?

your sam file are probably missing a sam header.... What is the output of

head -n1 file.sam

[WouterDeCoster]

1. Make sure you have a recent version of samtools installed
2. samtools view file1.sam -o file1.bam

Answer 1

[ATpoint]

Your command is wrong. Samtools works like this:

## Option 1: use -o to write the output to a file
samtools view -b -o out.bam in.sam

## Option 2: write STDOUT to file:
samtools view -b in.sam > out.bam

You combined both commands, resulting in a corrupted file. I am not even sure if your input files are still OK. I would realign, completely avoiding SAM files using a pipeline:

alignment (...) | samtools view -b -o out.bam -

This will directly output a BAM file from your alignment. There is no need for SAM files. They only take up space. Alternatively, directly pipe the alignment into samtools sort:

alignment (...) | samtools sort -o sorted.bam -

From there, do the merge:

samtools merge out.bam file1.bam file2.bam

Make sure you have the current version of SAMtools installed.

[1311703846]

Good anwser, thanks a lot

Answer 2

[h.mon]

Just cat will produce a corrupt sam file. You have two options wiht samtools:

• samtools cat - work on for bam and cram files, and the sequence dictionary of the files being concatenated need to be identical

• samtools merge - work for sam, bam and cram, takes as input a sorted files, and outputs a sorted file