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Results tagged with samtools
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user 2355
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
8
votes
How to subset a BAM by a list of QNAMEs?
Using samtools 1.12 or greater:
samtools view -N qnames_list.txt -o filtered_output.bam input.bam
OLD ANSWER:
When it comes to filter by a list, this is my favourite (much faster than grep):
# given a … bam file "aln.bam" and a list of read names "reads.txt":
samtools view -h aln.bam \
| awk 'FNR==NR {reads[$1];next} /^@/||($1 in reads)' reads.txt - \
| samtools view -b - > filtered_aln.bam
Basically …
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