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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURV only printing SV from one caller when SVTYPE is different from different callers #160

Open tkoganti opened 2 years ago

tkoganti commented 2 years ago

Hello there,

I have a question regarding SURVIVOR merge. I am using Manta and PINDEL as two callers. I want to merge SV calls that are present in both Manta and PINDEL. For this option - Take the type into account (1==yes, else no), I am using 1. So if there is an SV call with different SVTYPE in two different callers, I was assuming that SURV will print both calls in output. Instead it is only picking the call from PINDEL.

Here is an example -

This is the VCF line from Manta (SVTYPE=INS)- chr21 36164604 MantaINS:0:106:106:0:10:0 G <INS> . PASS END=36164605;SVTYPE=INS;LEFT_SVINSSEQ=GGCGCGCGCCCCCCCCCCAGGAGAAAAGGTAGGAGCCCGCCC;RIGHT_SVINSSEQ=TGGTGGGGTTGGTGCCGGGGGGCTGGTGGCGGGGGGGCGC PR:SR 31,0:1023,416

This is the lines from PINDEL (notice SVTYPE=RPL)- chr21 36164604 . GAGCGCTC GCGGCCGACCCCCCCCCCAACGAGAACTGGGACTCGACCGCCGAGGCGCCCGCGGTCACGGGGTAGGGTGGCGGGCTGGCTTGGAACGG . PASEND=36164611;HOMLEN=0;SVLEN=-7;SVTYPE=RPL;NTLEN=88 GT:AD 0/0:816,1

This is my SURV command - $SURVIVOR/SURVIVOR merge input.txt 1 1 1 1 1 0 output.vcf

This is the output VCF line. SVTYPE is showing up as NA and only PINDEL line showing up in the output(See SUPP=1) - chr21 36164604 . GAGCGCTC GCGGCCGACCCCCCCCCCAACGAGAACTGGGACTCGACCGCCGAGGCGCCCGCGGTCACGGGGTAGGGTGGCGGGCTGGCTTGGAACGG . PASSUPP=1;SUPP_VEC=01;SVLEN=81;SVTYPE=NA;SVMETHOD=SURVIVOR1.0.7;CHR2=chr21;END=36164685;CIPOS=0,0;CIEND=0,0;STRANDS=++ GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN ./.:NA:81:0,0:++:.:NA:.:GAGCGCTC:GCGGCCGACCCCCCCCCCAACGAGAACTGGGACTCGACCGCCGAGGCGCCCGCGGTCACGGGGTAGGGTGGCGGGCTGGCTTGGAACGG:chr21_36164604-chr21_36164685

The line from Manta is not showing up in output VCF (REF and ALT look like the line is coming from PINDEL VCF). Since they both have different SVTYPE, I was expecting SURV to not merge these and give two lines in output? Is this the expected behavior of the tool?

Appreciate your response on this. Thanks!

lgmgeo commented 2 years ago

Hi,

I have a similar question.

I have 2 VCF describing the same SV coordinates: 1 VCF with a DEL (chr2:3529001-3529901 DEL) and 1 VCF with a DUP (chr2:3529001-3529901 DUP). Here is my command line:

$SURVIVOR merge sample_files 300  1 1 1 0 50 sample_merged.vcf

So SURVIVOR should take into account the SV type (1==yes).

Surprisingly, only 1 SV is reported in the sample_merged.vcf output: the DUP. I was expecting SURVIVOR not to merge these 2 SV and give two lines as output... Moreover, why report the DUP rather than the DEL? Really strange for me.

Thank you for any help you can provide, Best, Véronique