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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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Matches to the reference instead of missing data #6

Closed MehmetGoktay closed 4 years ago

MehmetGoktay commented 4 years ago

Hi,

I would like to use Jasmine to merge Sniffles vcf outputs. The major problem I see is that, Jasmine most of the times it only outputs missing data for the samples that did not identify SV entries.

Is there a way to force Jasmine to check if it is a real missing data or matches to the reference 0/0? Or should I treat any missing data as matches to the reference after using Jasmine?

Like this example: Chr3 5797105 0_4943 GTTCAATCTTCGTCTTGTTTCTATTTGAGATTGAAGTTGAAATTATGCTCGATCTGTTCTGTAGCTAGAATT N . PASS PRECISE;SVMETHOD=JASMINE;CHR2=Chr3;END=5797176;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=4.523800;Kurtosis_quant_stop=1.082952;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-71;STRANDS=+-;RE=81;REF_strand=0,0;AF=1;STARTVARIANCE=0.000000;ENDVARIANCE=0.000000;AVG_LEN=-72.000000;AVG_START=5797105.000000;AVG_END=5797177.000000;SUPP_VEC_EXT=1010000010000;IDLIST_EXT=4943,5641,6674;SUPP_EXT=3;SUPP_VEC=1010000010000;SUPP=3;IDLIST=4943,5641,6674 GT:IS:OT:OS 1/1:.:DEL:. ./.:NA:NA:NA 1/1:.:DEL:. ./.:NA:NA:NA ./.:NA:NA:NA ./.:NA:NA:NA ./.:NA:NA:NA ./.:NA:NA:NA 1/1:.:DEL:. ./.:NA:NA:NA ./.:NA:NA:NA ./.:NA:NA:NA ./.:NA:NA:NA

Best Regards, Mehmet

mkirsche commented 4 years ago

Hi Mehmet,

Jasmine will only output missing data (./. genotype) if there is no vcf entry in a particular sample at that site. If there is a 0/0 entry present in the input data, the same 0/0 genotype will be output.

As for interpretting the output, it's generally safe to assume that the lack of a variant call corresponds to a match to the reference. Checking for 0/0 genotypes and filtering those out can be done either before or after running Jasmine

Hope that answers your question! Melanie

MehmetGoktay commented 4 years ago

Hey Melanie.

Yes it does.

Thank you very much, Mehmet