how to understand the output, MELT result as input

clemgoub / TypeTE

Genotyping of segregating mobile elements insertions

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how to understand the output, MELT result as input #5

Closed GGBond178 closed 11 months ago

GGBond178 commented 12 months ago

we used the melt output file as input.

the output folder include

samples
RM_intervals.out
output_TSD_Intervals.out
locusAlleles
genotyping_logs
RM_insertions_TSD_strands
OUTPUTS_Ref_testdata.TypeTE.vcf.gz
OUTPUTS_Ref_testdata.input
OUTPUTS_Ref_testdata.allele

how to understand the output? for example, OUTPUTS_Ref_testdata.TypeTE.vcf.gz file, how to know if the allele "PASS" the QC or not？

The original MELT output has QUAL column.

clemgoub commented 11 months ago

Hello!

We did not implement specific QC filters with TypeTE. However you should have access to the number of reads mapped per allele. Could you post 1-2 lines of your ouput VCF, so I can point you to it?

Note that if you are working with reference loci, I recommend you to use TypeREF, that should be more streamlined and also allows you to deal with L1 and SVA. https://github.com/clemgoub/typeref -- we have a tutorial available here: https://link.springer.com/protocol/10.1007/978-1-0716-2883-6_4

Best,

Clément

GGBond178 commented 11 months ago

Thank you for your valuable guidance!The issue I previously encountered has been successfully resolved.

Best,

Yue