samFilter(1) filter nucleotide sequence alignments in SAM files

SYNOPSIS

samFilter file.sam reference.fasta out.sam [options]

OPTIONS

file.sam
Input SAM file.
reference.fasta
Reference used to generate reads.
out.sam
Output SAM file.
-minAlnLength value
(50) Report alignments only if their lengths are greater than value.
-minAlignLength value
Alias of -minAlnLength
-minLength value
Alias of -minAlnLength
-minPctSimilarity value
(70) Report alignments only if their percentage similairty is greater than value .
-minPctIdentity value
Alias of -minPctSimilarity
-minPctAccuracy value
(70) Report alignments only if their percentage accuray is greater than value.
-minAccuracy value
Alias of -minPctAccuracy
-hitPolicy value
(randombest) Specify a policy to treat multiple hits from [all, allbest, random, randombest, leftmost]
all
report all alignments.
allbest
report all equally top scoring alignments.
random
report a random alignment.
randombest
report a random alignment from multiple equally top scoring alignments.
leftmost
report an alignment which has the best alignmentscore and has the smallest mapping coordinate in any reference.
-scoreSign value
(-1) Whether higher or lower scores are better.
-1
lower is better
1
higher is better.
-scoreCutoff value
(INF) Report alignments only if their scores are no worse than value.
-seed value
(1) Seed for random number generator. If seed is 0, then use current time as seed.
-holeNumbers value
A string of comma-delimited hole number ranges to output hits, such as '1,2,10-12'. This requires hit titles to be in SMRT read title format.
-smrtTitle
Use this option when filtering alignments generated by programs other than blasr(1), e.g. bwa-sw or gmap. Parse read coordinates from the SMRT read title. The title is in the format ,/name/hole/coordinates/, where coordinates are in the format \d+_\d+, and represent the interval of the read that was aligned.
-titleTable value
Use this experimental option when filtering alignments generated by blasr(1) with -titleTable titleTableName, in which case reference titles in SAM are represented by their indices (e.g., 0, 1, 2, ...) in the title table.
-filterAdapterOnly value
Use this option to remove reads which can only map to adapters specified in the GFF file.
-v
Be verbose.

NOTES

Because SAM has optional tags that have different meanings in different programs, careful usage is required in order to have proper output. The "xs" tag in bwa-sw is used to show the suboptimal score, but in PacBio SAM (blasr(1)) it is defined as the start in the query sequence of the alignment. When -smrtTitle is specified, the xs tag is ignored, but when it is not specified, the coordinates given by the xs and xe tags are used to define the interval of a read that is aligned. The CIGAR string is relative to this interval.