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FelixKrueger / SNPsplit

Allele-specific alignment sorting
http://felixkrueger.github.io/SNPsplit/
GNU General Public License v3.0
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'S' CIGAR operation not allowed #36

Closed brainfo closed 3 years ago

brainfo commented 4 years ago

I aligned reads using Bowtie2, and when SNPsplit read the bam file, it said: Found CIGAR operations other than M, I, D or N: 'S'. Not allowed at the moment Should I specify any parameter when running Bowtie2 or filter the input reads in some reads to rule out "S" type reads? Could I just filter the sam file to get alignments other than 'S' alignments? Does this differ with specify --end-to-end. when using Bowtie2?

FelixKrueger commented 4 years ago

The current released version does indeed not allow reads to be soft-clipped, --end-to-end would be better. I have in the meantime added support for softclipping as well though, but it is still in the development version. You could try to clone it with git@github.com:FelixKrueger/SNPsplit.git, and give that a go?

FelixKrueger commented 4 years ago

The current released version does indeed not allow reads to be soft-clipped, --end-to-end would be better. I have in the meantime added support for softclipping as well though, but it is still in the development version. You could try to clone it with git clone git@github.com:FelixKrueger/SNPsplit.git, and give that a go?

brainfo commented 4 years ago

The current released version does indeed not allow reads to be soft-clipped, --end-to-end would be better. I have in the meantime added support for softclipping as well though, but it is still in the development version. You could try to clone it with git@github.com:FelixKrueger/SNPsplit.git, and give that a go?

Ok, I'll have a try. Thanks!

FelixKrueger commented 3 years ago

I hope it worked?