Extract the XS field from bam

[Yexzm]

Hello everyone,

BWA mem generates for each read an "XS" field (the suboptimal alignment score). When I use samtools view, it's presented this way :
- NS500801:90:HY7JVBGXY:2:21205:8003:11253 147 chrM 958 60 76M = 920 -114 CCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGG >>;@B@CC1C??=??AAC=???>C@C>CC@BAAA?@<>>>>>=B?BB@@@?A=B=B>>>><@A=B<=;A>=@=;>= BD:Z:IIIMPOLKNKJJJBIMOMIBBJLKKIKLMKJKJIIKHAAAAILKKKLJIHJKHHHH@@GGIHLLLKKLJCKOJLJJ PG:Z:MarkDuplicates RG:Z:id BI:Z:LLLPTSOOSROPQHOTSQOGGNPPQNQPROLPNMMNNFFFFLNNONPOMLNOMLMNEEKLNMOOPOONMHOROPNN NM:i:0 AS:i:76 XS:i:55

Does anyone know an easy way to extract it ? With R ? I mean I know I could use samtools view + awk but it'll take a long time.

Thanks in advance!

[lindenb]

using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

java -jar dist/bioalcidaejdk.jar -e 'stream().forEach(R->println(R.getAttribute("XS")));'  in.bam

[Yexzm]

Hi lindenb, thank you for your answer,

How can I get the read name too ? I would like to have a table the in the first column the read name, and in the second the XS.

[lindenb]

> How can I get the read name too ?

... printl(R.getReadName()+" "+R.getAttribute("XS")

[Yexzm]

Thank you very much for your help!

The output file is too big, I'm trying to get the chromosome too so that I can separate it per chromosome. I tried "getReferenceIndex" but it returns "null". Do you know how I could do ?