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Question: filter BAM file for reads that map 100% identity
1
gravatar for oriolebaltimore
2.9 years ago by
oriolebaltimore • 150
United States
oriolebaltimore • 150 wrote:

Hello, I have a BAM file and I want to create another BAM file by filtering only reads that are 100% identical mapped. For example if my read length is 100 , I want to select CIGAR 100M and make a bam file. Could you please suggest how this can be done. Thanks Adrian
samtools bam cigar • 1.9k views
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modified 2.9 years ago by h.mon ♦ 31k • written 2.9 years ago by oriolebaltimore • 150
2
gravatar for h.mon
2.9 years ago by
h.mon ♦ 31k
Brazil
h.mon ♦ 31k wrote:

To check for a given length of total match - e.g. 100 - you can use perl and anchor the regular expression: /^100M$/. This will exclude any other total match length (e.g. 95M or 125M) and any soft clipped read. You will have to re-header the file after filtering.

samtools view potexvirus2.bam \
    | perl -lane 'print if $F[5] =~ /^100M$/;'
ADD COMMENT • link modified 2.9 years ago • written 2.9 years ago by h.mon ♦ 31k
1
gravatar for Pierre Lindenbaum
2.9 years ago by
Pierre Lindenbaum ♦ 131k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 131k wrote:

using samjdk http://lindenb.github.io/jvarkit/SamJdk.html . Check the edit-distance (NM) exists and is equals to zero.

java -jar  dist/samjdk.jar -e 'return !record.getReadUnmappedFlag() && record.getCigarString().equals("100M") &&  (record.getIntegerAttribute("NM")==null || record.getIntegerAttribute("NM").intValue()==0);' in.bam
ADD COMMENT • link modified 2.9 years ago • written 2.9 years ago by Pierre Lindenbaum ♦ 131k

Depending on your aligner, NM may or may not include clipped bases so you'll probably want to check the CIGAR as well.

ADD REPLY • link written 2.9 years ago by d-cameron • 2.2k
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