Open woodoo46 opened 4 years ago
A little bit more information: ) I do not have sequence ) the output distance file is empty
Thanks!
Hi George. Thanks for reporting this. Why is "999" in your ALT field for the second file? I need to look at the code, but I think any line with invalid ALT entries will be skipped. Are there any errors reported in the ".log" file?
As another note, SVmerge will in general consider deletions without the sequence only when you have an "END" tag in the INFO field (which I see you do for both variants), and will only consider insertions if the inserted sequence is specified either in the ALT field or as a "SEQ=" INFO field entry.
Sorry the manta call was copied wrong, it should be like this: chr1 108190708 MantaDEL:180899:0:1:0:0:0 A \<DEL> 999 PASS END=108194629;SVTYPE=DEL;SVLEN=-3921.....
They all have END tag in the INFO field.
The log file is this:
2020/07/29 10:13:42 Calculating distances between neighboring variants in VCF files listed in test.fof 2020/07/29 10:13:42 Writing vcf file merge.test.fof.clustered.vcf of clustered variants 2020/07/29 10:13:42 Done
Thanks!
Hi there,
For testing, I made two vcf files, one file has record like this
chr1 108190704 DEL00000334 T \<DEL> . PASS IMPRECISE;SVTYPE=DEL;SVLEN=-3926;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr1;END=108194630 ...
and another file has only one record like this:
chr1 108190708 MantaDEL:180899:0:1:0:0:0 A \<DEL> 999 PASS END=108194629;SVTYPE=DEL;SVLEN=-3921;
Supposedly, they should be merged, since breakpoints are very close to each other (left side 4bp, right side 1bp). But the output file still has two records. Is this expected?
I ran the command as this:
SVmerge --fof ${filename} --ref $HG38
Thanks!
George