I am trying to use bamtools filter to keep output a new bam file with a specific sequence. This is what I am using...
bamtools filter -in Aligned.bam -queryBases AAACCTG >Aligned_1.bam
This does not return any matches. The question I am asking, is it possible to filter sequencing reads from a BAM file that has specific sequence of interest? If so, how? Are there any other tools that might be able to do this?
Thanks in advance for any guidance provided.
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written
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devin.porter92 •
samtools view -h input.bam | awk -F '\t' '($1 ~ /^@/ || $10 ~/AAACCTG/ )' | samtools view -Sb -o out.bam -
using samjs
java -jar dist/samjs.jar -e 'record.getReadString().contains("AAACCTG")' input.bam
Thanks a lot! I was able to make it work with the following:
samtools view -h input.bam | awk -F '\t' '($1 ~ /^@/ || $10 ~/AAACCTG/ )' >filter.sam ; samtools view filter.sam -Sb -o filter.bam
ah yes, I forgot to write the last hyphen on my command line. You should be able to write filter the bam without writing this 'filter.sam'.
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