If I run bwa bwasw like this:
~/src/bwa/latest/bwa/bwa bwasw -z 1000 ~/refs/human_g1k_v37.fasta cluster-14263.walks
I get back the positive hits from some of the sequences, but also the empty hits for the sequences that don't map anywhere:
cluster-14263-walk-35 16 4 44630869 0 3S3M3D10M2I6M9D18M1I12M5I22M2I4M26S * 0 0 CAAGTACAGCTTTTCACTGAGGCATGGAATAAATATCCATTATGGCTCTGAGTGCCCCCAGAATGCACTGCGCACCAGCGCCATGTTTTAGCTCAAGCATAACAACTCCTGACC * AS:i:31 XS:i:31 XF:i:1 XE:i:0 XN:i:0 cluster-14263-walk-36 4 * 0 0 * * 0 0 GGTCAGGAGTTGTTATGCTTGAGCTAAAACATGGCGCTGGTGCGCAGTGCATTCTGGGGGCACTCAGAGCCATAATGGATATTTATTCCATGCCTCAGTGGAAG * cluster-14263-walk-37 4 * 0 0 * * 0 0 GGTCAGGAGTTGTTATGCTTGAGCTAAAACATGGCGCTGGTGCGCAGTGCATTCTGGGGGCAT *
What is the cleanest/recommended way of saving only the hits and not the sequences that have no hit?
Sorry if this has been answered before, I couldn't find an answer other than grepping on the resulting files.
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The FLAG field has a bit for testing whether or not a read was "mapped". One can exclude unmapped reads as follows:
samtools view -F 0x4 aln.bam
~/bin/bwa bwasw -z 1000 $ref $reads | ~/bin/samtools view -F 0x4 -bt $ref.fai - > file.bam # Perfect! Thanks Aaron!
Good point drio. If you want to do "OR" logic such as this (-F 0x4 || MAPQ != 0), I would recommend bamtools' JSON "rules" files.
You can also use Picard tools. http://goo.gl/ndzYU Something like: java -jar picard/directory/ViewSam.jar INPUT=aln.bam ALIGNMENT_STATUS=Unaligned
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