How can I use samtools to identify discordantly paired reads or is it even possible? I can use awk to simply output reads which are mapped on different chromosomes, and also reads where the distance between the pairs is significantly larger than expected but is there a way to do this via samtools?
Question: Identifying discordantly mapped reads
1
Linda • 150 wrote:
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modified 2.8 years ago
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Pierre Lindenbaum ♦ 133k
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5.2 years ago by
Linda • 150
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iraun • 3.8k wrote:
There are different options:
- You can use samtools
and give as argument the following flag '-F 1294'. In this way you'll discard all reads having which are: read mapped in proper pair, read unmapped,mate unmapped,not primary alignment,read is PCR or optical duplicate.
- As you've mentioned, you can use awk
to extract mates mapped on different chr. You should convert your bam to sam, and then awk '($3!=$7 && $7!="=")'
.
I would vote for the first approach, because it includes the distance between pairs issue.
1
Pierre Lindenbaum ♦ 133k wrote:
using samjdk: http://lindenb.github.io/jvarkit/SamJdk.html
$ java -jar dist/samjdk.jar -e 'return record.getReadPairedFlag() && !record.getReadUnmappedFlag() && !record.getMateUnmappedFlag() && !record.getReferenceName().equals(record.getMateReferenceName());' in.bam
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just filter out flags 3854 ( http://broadinstitute.github.io/picard/explain-flags.html ) ? (
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