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SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\
| samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome

samtools index reads.bwa.targetGenome.bam

Count number of records (unmapped reads + each aligned location per mapped read) in a bam file:

samtools view -c filename.bam

Count with flagstat for additional information:

samtools flagstat filename.bam

Count the number of alignments (reads mapping to multiple locations counted multiple times)

samtools view -F 0x04 -c filename.bam

Count number of mapped reads (not mapped locations) for left and right mate in read pairs

samtools view -F 0x40 filename.bam | cut -f1 | sort | uniq | wc -l
samtools view -f 0x40 -F 0x4 filename.bam | cut -f1 | sort | uniq | wc -l #left mate
samtools view -f 0x80 -F 0x4 filename.bam | cut -f1 | sort | uniq  | wc -l #right mate

Remove unmapped reads, keep the mapped reads:

samtools view -F 0x04 -b in.bam > out.aligned.bam

Count UNmapped reads:

samtools view -f4 -c in.bam

Require minimum mapping quality (to retain reliably mapped reads):

samtools view -q 30 -b in.bam > aligned_reads.q30.bam
samtools view -q 30 -c in.bam #to count alignments with score >30

Require match to be on the sense strand of the reference (samtools flag)

samtools view -F 16

Require match to be on antisense strand (samtools flag)

samtools view -f 16

Require at least N matches at the start of the read:

$N=6
samtools view in.bam \
| perl -lane 'next unless $F[5] =~ /^(\d+)M/;print if $1 >= $N;'

Filter by number of mismatches in BWA generated output, use BWA-specific flag:

Tag Meaning
NM Edit distance
MD Mismatching positions/bases
AS Alignment score
BC Barcode sequence
X0 Number of best hits
X1 Number of suboptimal hits found by BWA
XN Number of ambiguous bases in the reference
XM Number of mismatches in the alignment
XO Number of gap opens
XG Number of gap extentions
XT Type: Unique/Repeat/N/Mate-sw
XA Alternative hits; format: (chr,pos,CIGAR,NM;)*
XS Suboptimal alignment score
XF Support from forward/reverse alignment
XE Number of supporting seeds

To keep only reads that map without any mismatches:

bamtools filter -tag XM:0 -in reads.bam -out reads.noMismatch.bam

Retain only uniquely mapping reads (reads with a single unambigous mapping location):

If BWA was used it is possible to use the BWA XT flag value U for unique (analogously, R is for repeat). I did not find a simple way to do this with samtools or bamtools, so grep to the rescue:

samtools view reads.bam | grep 'XT:A:U' | samtools view -bS -T referenceSequence.fa - > reads.uniqueMap.bam

However, the concept of "uniquely mapping" is not the cleanest idea - in most scenarios any given read could be placed elsewhere although it may be a lower scoring alignment. Thus, you could instead filter based on mapping quality, to retain the "reliably mapped" reads. Different mappers have different scoring models. As a rule of thumb, min values of 5 or 10 will work well. If you used bowtie/bowtie2, try:

samtools view -b -q 10 foo.bam > foo.filtered.bam