samFilter - Online in the Cloud

PROGRAM:

NAME

samFilter - 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.

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