[Boel]

Dear Dave,

In principle, Pindel works also for overlapping paired-end reads, even for single end reads.

You may need to do the following to achieve a better result:
1. extract reads with bam2pindel.pl (http://www.ebi.ac.uk/~kye/pindel/v_0..._PINDEL.tar.gz) as the internal BAM input function of Pindel may break (or need some changes);
2. modify the coordinate in the extracted records by shifting one read length.
Say read length is 105 and you saw:
@readn
AGGTAATA...
+ chr1 10000 60 200 sample1

change the third line to
+ chr1 9900 60 200 sample1

If you saw "-", put 10100 there, for example.

3. run Pindel (source code at https://trac.nbic.nl/pindel/)

Good luck and send me an email if you have any questions.

Kai

I don't understand what the purpose or effect of this manipulation would be, could someone please explain? Also, is this still necessary in the latest release of pindel? I have overlapping paired end reads and pindel seem to be working on them just fine (so far), I am using the configuration file approach.

Thanks,
Boel

[mikhmv]

convert from pindel vcf to dindel format

I ended up with following script:

cat XXXX_D.vcf | grep DEL | awk '{print $1,"\t",$2,"\t&&&"$4}'| sed -e 's/&&&./-/'> XXXX_D.dindel.del
cat XXXX_SI.vcf | grep INS | awk '{print $1,"\t",$2,"\t&&&"$5}'| sed -e 's/&&&./+/' > XXXX_SI.dindel.ins
cat XXXX_D.dindel.del XXXX_SI.dindel.ins > XXXX.dindel.pindel

and added this file (by cat XXXX >>) to Dindel output from the first step.
Regards,
and thanks to Heisman for a help

[mikhmv]

Pindel to Dindel

I made improved version of script.

I have a several questions to someone who know how dindel work:
1. Can we replace INV on DEL+INS?
2. Can we do the same for RPL and TD?
3. Do we need to change coordinates (say +1 for INS or DELS)?

Improved code is here:

cat XXXX_D.vcf XXXX_INV.vcf XXXX_SI.vcf XXXX_TD.vcf | awk '/DEL/ {pos=$2+1; print $1,"\t",pos,"\t-"substr($4,2)}; /RPL|INV/ {pos=$2+1; print $1,"\t",pos,"\t-"substr($4,2)"\n"$1,"\t",pos,"\t+"substr($5,2)}; /INS/ {pos=$2+1; print $1"\t"pos"\t+"substr($5,2)}' > XXXX-all.pindel.dindel