User: pierre.peterlongo

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Posts by pierre.peterlongo

<prev • 99 results • page 1 of 10 • next >
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Comment: C: DiscoSNP++: reducing missing data for heterozygous species
... Hi, sorry for the delay, On regions with high variant density, discoSnp results depend on the 'b' option. With b 0 no variant is detected, with b 1 some of them are detected, and with b 2 almost all of them are detected (but with a high false positive rate on complex data). Once detected, we can ...
written 13 days ago by pierre.peterlongo680
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Answer: A: DiscoSNP++: reducing missing data for heterozygous species
... Hi Yann, I do not understand why this is an issue. Are you expecting those variants to be covered? The advice I can give you is to have a look to coverages themselves instead of genotype only. The threshold used to determine whether a variant is missing ./. or not depends on the *solidity thresh ...
written 16 days ago by pierre.peterlongo680
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Answer: A: rank = 0 in DiscoSNP
... Hello, The rank value reflects how discriminant a variant is among a set of individuals (read sets). - If you've a unique read set, all rank value will be equal to zero, and this value is not informative - else, variants whose rank is equal to zero are variants that do not discriminate read set ...
written 24 days ago by pierre.peterlongo680
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Comment: C: discoSNP++ comparison of shared and unique variants between different samples wi
... Hi André, Your question is not clear to me, but I'm trying to answer it there: There is a threshold applied on kmers abundance (kmer seen less than T times are not considered in the graph) and there is a threshold for read coherency (once reads are mapped back on alleles, we verify that each all ...
written 8 weeks ago by pierre.peterlongo680
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Comment: C: Understanding DiscoSNP++ output VCF file
... `./.` (for read set `i`): the variant whose id is *SNP_higher_path_9480770* has not enough corresponding reads in the read set `i`. *not enough* means that both alleles are not read coherent (cf *read coherent* definition in the publication) Pierre ...
written 10 weeks ago by pierre.peterlongo680
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Answer: A: Understanding DiscoSNP++ output VCF file
... Hi Achal, thanks for your question. Here is an explanation (non limited to discoSnp, and adapted to diploid species). A genotype provides a way to know for each variant if it exists in the reference allele and/or in the alternative allele. - with a `/` : - with a reference genome: the first ...
written 10 weeks ago by pierre.peterlongo680
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Comment: C: discoSNP++ comparison of shared and unique variants between different samples wi
... Thanks for your message André, Your commands look perfect. For kissreads steps, you may remove the `-coverage_file 270X-discoSNP-5th-RUN_cov.h5` option. This one provides a solidity threshold per input read set (for coherent vs uncoherent variants distinction), but, as we hack here kissreads using ...
written 12 weeks ago by pierre.peterlongo680
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Answer: A: discoSNP++ comparison of shared and unique variants between different samples wi
... Hi all, Thanks André for asking your question here. This is a generic need, that should be more explicit in the documentation. There are two main ways to answer your question (in absence of a reference genome, else, simply use the -G discoSnp++ option to obtain variant locus). - Run discoSnp on ...
written 12 weeks ago by pierre.peterlongo680
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Answer: A: Calling SNPs with low coverage
... Hi there, Maybe it's a bit late, but I'd like to highlight the [discoSnp][1] approach which might answer this initial question. Without reference genome, discoSnp may predict SNPs and Indels from raw NGS reads. It does not depend on read alignment process and may find low covered variants. It rem ...
written 3 months ago by pierre.peterlongo680
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Answer: A: ID field of discosnp++
... Hi - If the VCF file was created with a reference genome, it may appear that some predicted variants are not mapped on the genome. If it was created without a reference genome, none of them are mapped. When a variant is not mapped to a reference genome, the chrom field indicates the id of the pre ...
written 3 months ago by pierre.peterlongo680

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