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@mari-ga and @wxicu please modify the section on minimum required inputs following this:
The hashing and genetic mode are two independent workflows, and the rescue mode allows to perform joint demu…
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I'm trying to understand what the added fields T, E, GO, and GN are in the vcf output by `consensus.py` (`cluster_genotypes.vcf`) I don't see these tags in the output from freebayes, and that they're …
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Review existing tools in the pipeline if they can take in Nanopore data. If not, find a suitable alternative for long reads.
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Hi!
FreeBayes reports 4 INFO fields that are used to assess strand and read placement bias.
> ##INFO=
##INFO=
##INFO=
##INFO=
Graphical illustration:
![ngs_biases_short](https://user-im…
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Hi Marcel,
I'm sorry for the additional issue, but I just wanted to ask if it was normal to have a significant number of unphased reads (specifically 99.99% of reads were unphased). I installed wha…
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Hi:
my data , F1 , tetraploid , 7 chromosomes , NGS data , BWA and GATK haplotype .
there is not 7 linkage groups , just like one .
Your paper used the SNP array data ,and said "Dosage estimatio…
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We need to use the same gene region when switching between refseq and gencode to avoid different scales as illustrated:
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Hi here!
I'm computing with the script SARS-CoV-2-GISAID-freebayes.sh. Once at the stage of merging VCFs using jacquard, the same problem comes back every time, even with less than 3000 VCFs files…
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Input: PacBio long read, HiC and Illumina short read data
Assembly: Canu v2.1.1 and then run my assembly through purgeHaplotigs
Variants: FreeBayes
I process HiC and PacBio files as recommended …
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