Combine multiple samtools view

Question

[rah]

Can anyone help me with combining two samtools view commands into a single command.

I need to remove some alignment tags "XA and SA" and afterwards i also need to keep only the aligned reads to the "canonical" chromosomes from a reference genome.

It is possible to do all of this in multiple steps as so (with index created in between):

1) remove tag - taken from other biostar posts.

samtools view file.bam | grep 'XA\|SA' | cut -f 1 > discard_ID.txt

samtools view -h file.bam | fgrep -vf discard_ID.txt | samtools view -Sb - > out.bam

2) extract aligned reads

samtools view -F 4 -q 30 out.bam chr{1..22} chrX chrY chrM -b > final.bam

But i would like to combine these into a single command. So i've tried the following

samtools view -h file.bam | fgrep -vf bad_names.txt | samtools view -F 4 -q 30 - chr{1..22} chrX chrY chrM -b > test.bam

the problem is the different intermediate bam files are of course not index, so is there a way to combine 1) and 2) into a single command. I've also tried adding the -h option to samtools view to see if the output with header is able to be passed on in the pipe.

Thanks a lot

[Pierre Lindenbaum]

samtools view file.bam | grep 'XA\|SA' | cut -f 1 > discard_ID.txt

that's wrong. you would delete any read with a name containing XA.

[rah]

yeah sorry for the mistake, thats what i meant by filtering out. I want to remove all the reads with XA and SA tag. Afterwards i want to extract all the reads which aligns to chr 1-22, x,y,m

Answer 1

[Pierre Lindenbaum]

using samjdk : http://lindenb.github.io/jvarkit/SamJdk.html

samtools view -F 4 -q 30 - chr{1..22} chrX chrY chrM -u | \
java -jar dist/samjdk.jar -e 'Object att = record.getAttribute("XA"); if(att==null)  att = record.getAttribute("SA");  return att==null ;'