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
•
written
by
oriolebaltimore
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 $F[5] =~ /^100M$/;'
Hi, Could you please tell me how I could do the opposite? How to keep only 100% id mapped reads?
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
Log in to answer this question.
