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Hello,
Can you please provide some more details on the format of graphtyper output VCF? I'm interested essentially in 2 points:
1. Variants definitions. Take the following example:
Given my me…
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`singularity exec ~/software/pangenie/container/pangenie.sif PanGenie-index -v keepA_C_0.5missing_100kbub_phased_deleteN_id_trim_filtered_SVs.vcf -r ZS11.genome.fa -t 24 -o PanGenie`
My vcf sequ…
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**TLDR:** Ring mod causes frequencies above the audible frequency range that could result in audible harmonics because the sample rate is not twice as high as them.
**Impact:** Medium to low
**Feasi…
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Hi
I am trying to run viva on windows after intall Julia 1.7.2 .
I launch viva in the powershell with:
viva -f AMvsJJref.vcf -s pdf -o .
After a julia open and load packages, only 1 second aft…
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I have a question concerning the recommended workflow.
I used short reads to create the input VCF file and the ont long reads in whatshap.
I used the pipeline below but my haplotype a nearly the s…
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For some reason, when I generate reads using a VCF, most of the threads exit without a sound a few minutes after starting the thread. This seems to happen before the reads are assigned parts of the ge…
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Hi,
Does whatshap works with the vcf file generated by longshot? I am getting following error.
my command: whatshap phase --ignore-read-groups --reference Asm.pa_ctg.fasta Asm.pa_ctg_bwa_sorted_l…
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Hello,
How can I adress this error ?
Error in hapmap_parser_map(hmp_file[1], out) :
ERROR: Wrong HAPMAP file, no line begin with "rs#".
The first line of my file starts with rs# so I do …
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I followed the given pipeline to create vcf file from parsnp to further use it for genotyphi.. Commands runs ok but not creating vcf file. any help ?
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Dalliance does a nice job of this.
danvk updated
9 years ago