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Question: Identifying discordantly mapped reads
1
gravatar for Linda
4.1 years ago by
Linda • 150
India
Linda • 150 wrote:

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?
samtools bam paired-end • 3.6k views
ADD COMMENT • link •
modified 20 months ago by Pierre Lindenbaum ♦ 124k • written 4.1 years ago by Linda • 150
1

just filter out flags 3854 ( http://broadinstitute.github.io/picard/explain-flags.html ) ? (     read mapped in proper pair
    read unmapped
    mate unmapped
    not primary alignment
    read fails platform/vendor quality checks
    read is PCR or optical duplicate
    supplementary alignment )

ADD REPLY • link written 4.1 years ago by Pierre Lindenbaum ♦ 124k
2
gravatar for iraun
4.1 years ago by
iraun • 3.6k
Norway
iraun • 3.6k 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.
ADD COMMENT • link written 4.1 years ago by iraun • 3.6k
1
gravatar for Pierre Lindenbaum
20 months ago by
Pierre Lindenbaum ♦ 124k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 124k 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
ADD COMMENT • link written 20 months ago by Pierre Lindenbaum ♦ 124k
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