I am running Pindel against 30x coverage whole exome data then using the conversion utility to create vcf files from the Pindel outputs. I get a number of results. I can correlate the _D, _INV, _SI, _TD files with deletions,inversions, short insertions and tandem duplicates. I do not have _BP, _LI or _CloseEnd results that I might expect - well maybe my data, no problem.
However I do have _Int, _IntFinal and _Rp results....though my vcf files are header only, no vcf lines.
What is the meaning of the _Int, _IntFinal and _RP files?
Which SVs do they represent?
Why do I get a vcf file with just a header? I would expect that if I don't get a result file for Bps (breakpoints) because none are found in my data, then the same should be true for "RP" whatever that is.
Thank-you for your help.
0 answers
No answers yet.
Log in to answer this question.
-
bcftools isec output for multiple vcf files interpretations
written by minoo •
-
Depth of coverage in Bam file does not match depth in VCF file
written by jsneaththompson
-
Broken vcf header, no column name?
written by samuel.lipworth •
-
Pairwise comparisons between multiple groups with DESeq2
written by lazappi •
-
pindel _RP and duplictation problem
written by jack1 •
-
Problem for pindel2vcf to create VCF file from pindel created _D files
written by hongbing.li •
-
Sorting with vcftools for tabix gone wrong
written by axelwilhelm
-
bcftools merge segmentation fault?
written by atruong •
-
Filtering Pindel Results
written by Dawe
-
Problem Assembling Breakdancer Output With Tigra
written by roalva1
Having the same issue 2.7 years later! Did you find out? Can you comment?