BAMADAPTERFIND(1) | General Commands Manual | BAMADAPTERFIND(1) |
bamadapterfind - find adapter contamination in sequencing reads
bamdapterfind [options]
bamdapterfind scans a BAM file for contaminations by sequencing adapters. It uses two separate methods for this detection:
s0s1s2s3s4s5s6s7s8s9s10s11s12s13s14s15s16t0t1t2t3
x3x2x1x0s0s1s2s3s4s5s6s7s8s9s10s11s12s13s14s15s16
where an infix s0s1s2... of the first read matches a suffix of the reverse complement of the second read. In this case it is likely that the first read has been sequenced beyond the end of the payload sequence and into the attached adapter. This overlap needs to be at least MIN_OVERLAP bases long to be considered. If such an overlap is found, then the adjacent sequences are checked for a match, where in the example x3x2x1x0 needs to be the reverse complement of t0t1t2t3. The adjacent sequences are checked up to a limit of ADAPTER_MATCH base pairs. If such a match is found then the auxiliary field ah is set to 1 and a3 is used to store the length of the suspected adapter sequence.
The following key=value pairs can be given at the program start:
level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are
If libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value is
verbose=<1>: Valid values are
mod=<1048576>: if verbose=1 then this sets the frequency of progress reports, i.e. a report is given for each mod'th input read/alignment
adaptersbam=<>: file name of the BAM file containing the list of adapter used for the adapter matching described above under list. The program contains an internal list which is used if this key is not given.
SEED_LENGTH=<12>: length of the seed used for detecting overlaps in overlap based matching (see overlap above, default value is 12 base pairs).
PCT_MISMATCH=<10>: percentage of mismatches allowed for overlap matching. This only includes the overlap, not the suspected attached adapter sequence. The default value is 10.
MAX_SEED_MISMATCHES=<SEED_LENGTH*PCT_MISMATCH>: maximum number of mismatches allowed in the seed. By default this value is computed as SEED_LENGTH*PCT_MISMATCH.
MIN_OVERLAP=<32>: minimum length of overlap for overlap matching in base pairs (see above). The default value is 32.
ADAPTER_MATCH=<12>: maximum number of base pairs to check for matching adapters in overlap based matching. The default value is 12.
adpmatchminscore=<16> minimum score for list based adapter matching (see above, default value is 16)
adpmatchminfrac=<0.75> minimum fraction of adapter sequence which needs to match (see above, default value is 0.75=75%)
adpmatchminpfrac=<0.8> minimum fraction of overlap for adapter list matching (see above, default value is 0.8=80%)
clip=<0> clip the adapters off and move the corresponding sequence part to the qs auxiliary field and the corresponding quality string part to the qq auxiliary field
reflen=<3000000000> length of reference sequence/genome
pA=<0.25> relative frequency of base A in reference sequence/genome
pC=<0.25> relative frequency of base C in reference sequence/genome
pG=<0.25> relative frequency of base G in reference sequence/genome
pT=<0.25> relative frequency of base T in reference sequence/genome
Written by German Tischler.
Report bugs to <germant@miltenyibiotec.de>
Copyright © 2009-2013 German Tischler, © 2011-2013
Genome Research Limited. License GPLv3+: GNU GPL version 3
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it. There is NO
WARRANTY, to the extent permitted by law.
July 2013 | BIOBAMBAM |