User: AGE

gravatar for AGE
AGE20
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2 days, 15 hours ago
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9 months, 3 weeks ago
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a******************@mail.mcgill.ca

Posts by AGE

<prev • 15 results • page 1 of 2 • next >
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Filtering for homozygous reference alleles
... I would like to obtain a gvcf file for non-variant sites with a minimum coverage of 5x (homozygous reference alleles that I can at least minimally trust). The non-variant sites i am getting seem to be of low coverage. For example a non-variant site with DP=51 but DP4=1,0,0,0. The bam file was filter ...
genome bioinformatics sequence snp written 14 days ago by AGE20 • updated 11 days ago by Biostar ♦♦ 20
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bcftools call error "--gvcf output mode requires FORMAT/DP tag, which is not present in the input header"
... I would like to get non-variant sites using bcftools but am getting an odd error about the DP field. bcftools mpileup -f genomic.fa file.bam | bcftools call --gvcf 5 -m > gvcf.vcf --gvcf output mode requires FORMAT/DP tag, which is not present in the input header Yet, the DP field is ...
sequence snp written 15 days ago by AGE20
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Comment: C: SSPACE assembling Genome!
... can you give an example of what your library.txt file looked like? ...
written 5 months ago by AGE20
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Comment: C: mpileup format to vcf
... It worked with the pipe > bcftools mpileup -f genomic.fa file.bam | bcftools call -vm > > file_var.vcf ...
written 5 months ago by AGE20
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Comment: C: is 1.4 Gb too large a genome for SPAdes?
... Thanks for the info! Yes, it does use quite a bit of RAM. I tried running the program a few weeks ago and it estimated that I needed 500Gb of RAM. ...
written 5 months ago by AGE20
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Comment: C: is 1.4 Gb too large a genome for SPAdes?
... I have access to a cluster. The program estimated that I need approx. 500G of ram last time it ran out of memory. ...
written 5 months ago by AGE20
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is 1.4 Gb too large a genome for SPAdes?
... I want to assemble a reptile genome with the software spades since it has given me no problems installing, unlike many other programs (e.g. Masurca, velvet, SOAPdenovo, etc). I'm wondering if a diploid genome of size 1.4 Gb is too large for this program. ...
genome assembly written 5 months ago by AGE20 • updated 5 months ago by h.mon27k
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Comment: C: mpileup format to vcf
... I tried this: > bcftools call -v -c file.mpileup > file.vcf > > Note: none of --samples-file, --ploidy or --ploidy-file given, > assuming all sites are diploid Failed to open file.mpileup: unknown > file type ...
written 5 months ago by AGE20
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Comment: C: mpileup format to vcf
... Yes, I got an error, saying failed to open pathto/file.mpileup ...
written 5 months ago by AGE20
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mpileup format to vcf
... I'm wondering if there's a simple way to convert directly from mpileup format to vcf without having to go through all the steps of creating a bam files to bcf to vcf etc. https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf I just ...
next-gen samtools snp written 5 months ago by AGE20

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