Hello,

I am mapping my reads with an aligner that allows for large indels (bbmap, other suggestions welcome).

I am than using SamJs to get reads that have large indels >1kb

java -jar ${HOME}/programs/jvarkit/dist/samjs.jar --file get_indel_sam_filter.javascript --samoutputformat SAM -o Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_Indel-1kb_v2.sam Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped.sort.bam

Java script used, cat get_indel_sam_filter.javascript :

function accept(rec) {
if(rec.getReadUnmappedFlag()) return true; 
var c=rec.getCigar(); if(c==null) return true; 
for(var i=0;i< c.numCigarElements();++i) {
var ce=c.getCigarElement(i);
if(ce.getLength()<1000) continue;
var s=ce.getOperator().name(); 
if( s=="D") return true; 
} return false;
}accept(record)

Now I would like to get a coordinate file with the start and end location of indels. For instance this record:

HWI-D00104:276:C6U65ANXX:7:1207:20052:96123 1:N:0:TTAGGC    0   Copenhagen_M35027   113671  38  89=11532D36=    *   0   0   TTTTTAACAGTTTGAGGTTTTAGATTTTTAGTTACAGAAGTGATATCGAATATTTTATCCAAAAAGAATGAGTAATTAATTGTCTTAGAAACGTCAACAACGAGAAAAAAGATTTAATATTACAG   BBBBBFFFFBFFFFFFFFBFFFFFF/BFF<<FFFB/B/FFFFFF//BFBBBBFFFFFFFFFFBFFFFBB/FBFFFFFFB<FFBFBFF<FF/F/FBFF</B</BFFBFFF/FF/<F////FBB/B7   AM:i:38 NM:i:11532

Has an indel between 113759 and 125292.

I am not sure if there is already a tool that easily finds these. Ideally, the cigar string before and after the indel is an 100% match (like in the example record).

Thanks.