Can someone clarify if clipping and masking are the same thing?
I see an undocumented bwa -s option to disable clipping:
http://www.biostars.org/p/62544/
I'm trying to see if I can disable masking to run stacks:
Several alignment programs allow the ends of reads to be implicitly trimmed by soft-masking them (converting the bases to Ns). The pstacks program will convert nucleotides that were soft-masked during alignment (this operation is recorded in the CIGAR string) into literal Ns, so that they do not improperly contribute to SNP calling. Users should beware, however, because some seed-based aligners (BWA and GSNAP) perform terminal alignments, in which large fractions of either end of a read can be soft-masked (all but the matching seed). This can result in alignments where only a fraction of the read was truly aligned to the reference and can have strange effects, such as the inability to call haplotypes despite the successful inference of SNPs, when depth of coverage is low. This behaviour can be turned off in some aligners (GSNAP).
http://onlinelibrary.wiley.com/doi/1...mec.12354/full
Can anyone confirm if the bwa samse -s is what I want?
Thanks!
I see an undocumented bwa -s option to disable clipping:
http://www.biostars.org/p/62544/
I'm trying to see if I can disable masking to run stacks:
Several alignment programs allow the ends of reads to be implicitly trimmed by soft-masking them (converting the bases to Ns). The pstacks program will convert nucleotides that were soft-masked during alignment (this operation is recorded in the CIGAR string) into literal Ns, so that they do not improperly contribute to SNP calling. Users should beware, however, because some seed-based aligners (BWA and GSNAP) perform terminal alignments, in which large fractions of either end of a read can be soft-masked (all but the matching seed). This can result in alignments where only a fraction of the read was truly aligned to the reference and can have strange effects, such as the inability to call haplotypes despite the successful inference of SNPs, when depth of coverage is low. This behaviour can be turned off in some aligners (GSNAP).
http://onlinelibrary.wiley.com/doi/1...mec.12354/full
Can anyone confirm if the bwa samse -s is what I want?
Thanks!