Luis Paulin comments

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                                            Luis Paulin

"--report_BND" and "--ignore_sd" params documented but unrecognized in Sniffles CLI

Thanks for the reports. For the case of `--ignore_sd` and `--report_BND` those parameters are for Sniffles 1, which has not been maintained for some time now. We updated part of...

Change name of sample in SNF file

@zaka-edd if the instructions above did not updated the samples names please let us know by re-opening this issue

Sniffles segfaults when output directory doesn't exist

Hi @ASLeonard v2.7 will check the immediate parent directory, if missing exits

Error in download

Dear @sybah2 can you please run the following command `conda info` in order to check if there are missing channels as the error message shows

--sample-id does not work in force calling mode

Hi @jules-o Sniffles genotyper only modifies the FORMAT/SAMPLE columns adding the genotype for the desired SVs based on the input VCF So the SAMPLE name is preserved from the original...

Request/Bug: Allow compressed reference

Thanks a lot

Very high proportion 0/1 genotype in DUP, BND and INV

For `DUP` and `BND` we expect the VAF/reported GT to be mostly heterozygous: DUP variant allele fraction for a 3x in a diploid organism is ~0.33, while 4x in a...

No variant reads reported with Sniffles2 genotyping

Dear Cheryl, the current version of Sniffles is able to detect the SV ``` 11 134595576 Sniffles2.DEL.0S0 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=-51;END=134595627;SUPPORT=5;COVERAGE=6,6,6,6,6;STRAND=+-;STDEV_LEN=0.000;STDEV_POS=0.000;SUPPORT_SA=0;VAF=0.833 GT:GQ:DR:DV 1/1:3:1:5 ``` However we see that the reported...

Pooled samples and mosaic option

Thanks for the additional information @SheepwormJM I out latest development version and found the DUP you mentioned marked with a filter and tagged as mosaic, which does not make much...