Merge multiple Sam files to one big Sam file. How?

Question

[jaqx008]

Hello everyone, I have a folder that contains among other files, a list of sam files that was split previously by someone else. I want to use the same file but in the un-split form so I am looking for a way to:

1. separate them out of the folder using grep because they are many (what grep command please?)
2. Merge them into one Sam file.

Thanks

Answer 1

[Medhat]

From sam to sorted bam: for f in *.sam; do filename="${f%%.*}"; samtools view -bS $f | samtools sort -@ 4 - ${filename}.sorted.bam; done Then you can merge them:

samtools merge out.bam in1.bam in2.bam in3.bam

So you can use:

samtools merge out.bam `ls *sorted.bam`

Source: http://www.htslib.org/doc/samtools.html

Note:

-@ for number of threads.
Instead of for loop you can use parallel; refer to this example:
A: Run Samtools on multiple files

[jaqx008]

the thing is I have hundreds of sam in the folder. it will take forever to do this one after the other to generate all bams before I merge them

[Medhat]

Then use parallel as suggested above

If you want use sam directly use MergeSamFiles from Picard tools:

java -jar picard.jar MergeSamFiles \ 
      I=input_1.bam \
      I=input_2.bam \
      O=output_merged_files.bam

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_sam_MergeSamFiles.php

[Friederike]

That's what screen or tmux are for. Coupled with parallel that should do the trick.

[jaqx008]

Im not an expert in this field, so some of the terms are strange to me. However, I will try to install picard and try the command. Thanks