SURVIVOR merge not working

[cccnrc]

I have 2 simple VCF CNV file to explore SURVIVOR, generated through GATK germline CNV , here the command I send

SURVIVOR merge \
            segments.vcf.list 1 -1 0 0 0 -1 segments.merged.vcf

Here segments.vcf.list:

cat segments.vcf.list 
/home/enrico/Dropbox/NY/twins_igan/GATK_CNV/PostGermlineCNVCaller_calls/A13665_PostGermlineCNVCaller/A13665.segments.vcf
/home/enrico/Dropbox/NY/twins_igan/GATK_CNV/PostGermlineCNVCaller_calls/A13661_PostGermlineCNVCaller/A13661.segments.vcf

And attached the 2 files (once compressed): A13661.segments.vcf.gz A13665.segments.vcf.gz

I get as output:

merging entries: 4016 merging entries: 3740

but the output file has only the header and no variant.

tail segments.merged.vcf
##FORMAT=<ID=LN,Number=1,Type=Integer,Description="predicted length">
##FORMAT=<ID=DR,Number=2,Type=Integer,Description="# supporting reference,variant reads in that order">
##FORMAT=<ID=ST,Number=1,Type=String,Description="Strand of SVs">
##FORMAT=<ID=QV,Number=1,Type=String,Description="Quality values: if not defined a . otherwise the reported value.">
##FORMAT=<ID=TY,Number=1,Type=String,Description="Types">
##FORMAT=<ID=ID,Number=1,Type=String,Description="Variant ID from input.">
##FORMAT=<ID=RAL,Number=1,Type=String,Description="Reference allele sequence reported from input.">
##FORMAT=<ID=AAL,Number=1,Type=String,Description="Alternative allele sequence reported from input.">
##FORMAT=<ID=CO,Number=1,Type=String,Description="Coordinates">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  A13665  A13661

Any idea why?

Thanks in advance for any help

[fritzsedlazeck]

I think that is something that I just fixed. The parser got confused if there is only an END tag in the info file.

Please download the code base and retry. Thanks Fritz

[cccnrc]

it works now! Thank you very much!