Dear all
I have a BAM file from Illumina whole genome data and I would like to filter out all the reads that fail Illumina's chastity filtering. From my understanding that is the flag 0x0200 (please correct me if you know differently). So to remove those reads and retain all other information in the BAM file can I just use samtools like this:
Many thanks
I have a BAM file from Illumina whole genome data and I would like to filter out all the reads that fail Illumina's chastity filtering. From my understanding that is the flag 0x0200 (please correct me if you know differently). So to remove those reads and retain all other information in the BAM file can I just use samtools like this:
Code:
samtools view -h -b -F 0x0200 input.bam > output.bam
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