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Hi @hannespetur,
We ran graphtyper2 using v2.5.1 two years ago to re-genotype SVs.
We noticed that vcf_merge in v2.5.1 does not include the --sv parameter.
Can we still merge the SVs across samp…
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Expected Behavior
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Implement flapjack-bytes to view genotyping information.
https://github.com/cropgeeks/flapjack-bytes
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Hi Claire,
Please, while running the genotyping_SV pipeline, I could not find the script "01_scripts/fasta_extract_flankingregions_claire.py" in the command "python3 ../01_scripts/fasta_extract_flan…
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Hi all
I'm trying to launch RetroSeq (using ubuntu os).
When I run the command line:
perl retroseq.pl -discover -eref ereff.tab -bam file_sorted.bam -output mysample.candidates.tab
I obtain this m…
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Hi Guys,
I use a valid read mapping on a valid vg graph for genotyping.
`g genotype -v -r path1 -q -S -p -t 8 graph.vg mapping.gam.index/ > calls.vcf`
The genotyping fails after augmenting the gra…
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I have called a bunch of samples with straglr and merged the (chrom, start, end, motif) beds into one unified bed. I would like to use this merged bed to genotype each sample again. Sometimes differen…
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I as wondering if svtyper does "joint genotyping" of multiple samples, analogous to what GATK does for SNPs?
Does svtyper do break-point resolution? For example, if I have a population samples with…
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Hi @hannespetur,
Sorry I might have missed this somewhere. Does Graphtyper perform SNV discovery from PacBio or Nanopore data or is this something still under development?
Thank you
Kind reg…
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It strikes me a bit odd that we support short/Short, long/Long, int/Integer, etc. but do not support char/Character. This has come up because I'm trying to store a boatload of genotyping values ('A', …