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Understand and identity the workflow of the vartable program.
Which part of the program depends on DNA-data and till where does this dependency continues.
- [ ] How to adjust vartable.py
- [ ] H…
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Hello @tjiangHIT, @Meltpinkg and cuteSV developers,
cuteSV v2.0.3 can produce malformed VCF output containing `R` nucleotides in the `REF` column. These are not allowed according to the [VCF v4.2 s…
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Hi,
I have read all your responses to question relating to "VCF" liftovers.
I understand the literal meaning of "CrossMap does NOT check if the reference allele is different from the alternate al…
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Dear @brentp,
thanks for the awesome tool. I'm just wondering if there is a way to convert *.somalier file to VCF/PED for performing additional analysis?
Thanks in advance,
Best regards,
…
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I got this error from subcommand haplotag in WhatsHap **2.2.dev9+g18b518d** ( Python 3.10.13 & pip )
> Found 1 sample(s) in input VCF
> Found` 1 sample(s) in BAM file
> ERROR: whatshap error…
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Filter by VCF FILTER == "PASS", or by any other combination of detected filters. Remember VCF's FILTER can be an array of filter strings.
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Similar to https://github.com/samtools/hts-specs/issues/403, I'd like to formalize the use of topology (especially for circular contigs) so that variants may span the origin of a circular contig witho…
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Hi Fritz,
I am trying to merge insertion variants from some vcfs and one of them is generated from DRAGEN.
Here is my SURVIVOR command:
`SURVIVOR merge input_ins_vcfs 1000 1 1 1 0 0 union6_ins…
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Hi Dariober
when I run with unmatched mode (the unmatched bam are merged from 10 un-related normal samples)
cnv_facets.R \
-t ./bams/S21-096.bam \
-n merged_normal.bam \
--unmatched \
-vcf v…
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Do you have an updated list of reference vcfs for b38?
genomeFasta_b37="human_g1k_v37.fasta"
refKnown1="Mills_and_1000G_gold_standard.indels.b37.vcf"
refKnown2="1000G_phase1.indels.b37.vcf"
dbs…
sph17 updated
10 months ago