Group: Unique Molecular Identifiers (UMIs)
Filters consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. Two kinds of filtering are performed:
Base-level filtering/masking is only applied if per-base tags are present (see CallDuplexConsensusReads and CallMolecularConsensusReads for descriptions of these tags). Read-level filtering is always applied. When filtering reads, secondary alignments and supplementary records may be removed independently if they fail one or more filters; if either R1 or R2 primary alignments fail a filter then all records for the template will be filtered out.
The filters applied are as follows:
When filtering single-umi consensus reads generated by CallMolecularConsensusReads a single value each
should be supplied for
When filtering duplex consensus reads generated by CallDuplexConsensusReads each of the three parameters may independently take 1-3 values. For example:
FilterConsensusReads ... --min-reads 10 5 3 --max-base-error-rate 0.1
In each case if fewer than three values are supplied, the last value is repeated (i.e.
80 40 ->
80 40 40
0.1 0.1 0.1. The first value applies to the final consensus read, the second value to one
single-strand consensus, and the last value to the other single-strand consensus. It is required that if
values two and three differ, the more stringent value comes earlier.
In order to correctly filter reads in or out by template, if the input BAM is not
queryname sorted or
grouped it will be sorted into queryname order. The resulting records are
coordinate sorted to efficiently
MD tags, and the output BAM is always written in coordinate order.
--reverse-tags-per-base option controls whether per-base tags should be reversed before being used on reads
marked as being mapped to the negative strand. This is necessary if the reads have been mapped and the
bases/quals reversed but the consensus tags have not. If true, the tags written to the output BAM will be
reversed where necessary in order to line up with the bases and quals.
|Name||Flag||Type||Description||Required?||Max Values||Default Value(s)|
|input||i||PathToBam||The input SAM or BAM file of consensus reads.||Required||1|
|output||o||PathToBam||Output SAM or BAM file.||Required||1|
|ref||r||PathToFasta||Reference fasta file.||Required||1|
|reverse-per-base-tags||R||Boolean||Reverse [complement] per base tags on reverse strand reads.||Optional||1||false|
|min-reads||M||Int||The minimum number of reads supporting a consensus base/read.||Required||3|
|max-read-error-rate||E||Double||The maximum raw-read error rate across the entire consensus read.||Required||3||0.025|
|max-base-error-rate||e||Double||The maximum error rate for a single consensus base.||Required||3||0.1|
|max-no-call-fraction||n||Double||Maximum fraction of no-calls in the read after filtering.||Optional||1||0.2|
|min-mean-base-quality||q||PhredScore||The minimum mean base quality across the consensus read.||Optional||1|