User: mernster

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mernster0
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Posts by mernster

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Comment: A: Haplotypic diversity with pegas package error
... I am struggling with the same issue. Did you get it solved? I think it could be caused by the sequences being to long perhaps? ...
written 8 months ago by mernster0
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Comment: C: Filtering for individual allelic balance in multisample vcf using GATK4
... DNA, average coverage is about 10 reads. I am working with very closely related species, thats why I wanted to keep the hets. My plan was to infer the phylogenetic tree using several methods (SNAPP, phylonet, Treemix and a concatenated tree with raxml) and then to compare the results. ...
written 9 months ago by mernster0
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Comment: C: Filtering for individual allelic balance in multisample vcf using GATK4
... I guess so. The original aim is to filter a multisample VCF by AB. The problem is, that if I do vcffilter -f 'AB > 0.25 & AB < 0.75 | AB < 0.01' input.vcf > output.vcf on a multisample VCF file, it uses the AB over ALL heterozygous genotypes in that site. However, what I want ...
written 9 months ago by mernster0
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Comment: C: Filtering for individual allelic balance in multisample vcf using GATK4
... thanks very much for the answer! I won't do that. But what do you advise me to do instead? Would you advise completely removing the genotypes of heterozygous individuals that are below/above the AB threshold? Doesn't that result in a huge loss of information? I have done a different kind of workfl ...
written 9 months ago by mernster0
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Filtering for individual allelic balance in multisample vcf using GATK4
... I have a multisample vcffile and would like to edit heterozygous individuals with a low or high allelic balance (AB). AB is defined as the ratio of reads showing the reference allele to all reads. If the AB is below 0.25, I would like to change the genotype to 1/1 (homozygous for alternateallele ). ...
vcf gatk gatk4 filtering written 9 months ago by mernster0 • updated 9 months ago by chrchang5237.1k
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Comment: C: concatenate VCFs with same sample set but with varying order
... Okay, I have tried java -jar $PICARD_HOME/picard.jar MergeVcfs I=35.vcf I=36.vcf O=all.vcf instead of java -jar $PICARD_HOME/picard.jar GatherVcfs I=35.vcf I=36.vcf O=all.vcf and it seems to work!! thank you very much ...
written 9 months ago by mernster0
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Comment: C: concatenate VCFs with same sample set but with varying order
... Hi Pierre, thanks for you answer! I tried picard GatherVcfs `java -jar $PICARD_HOME/picard.jar GatherVcfs I=35.vcf I=36.vcf O=all.vcf` The VCFs have the same sample IDs but in different order: `bcftools query -l 35.vcf` 14 11 13 12 3 6 10 7 9 5 8 2 4 1 `bcftools query -l 36.vcf` 5 9 11 13 2 ...
written 9 months ago by mernster0
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concatenate VCFs with same sample set but with varying order
... Hello, for each chromosome, I have a multisample VCF containing the same set of samples. However, the order of the sample columns varies among the VCFs. For example: VCF file 1: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 14 11 13 12 3 6 10 7 9 5 8 2 4 1 VCF file 2: #CHROM POS ID ...
vcf merge bcftools concatenate written 9 months ago by mernster0 • updated 9 months ago by Pierre Lindenbaum129k
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How to subset bamfile based on chromosome IDs
... Hi, I would like to subset a large bam file so that I can do the variant calling in parallel (using freebayes). I have tried to subset the bamfile based on subsets of the reference sequence. First, I subset the fasta reference sequence into fasta files containing the equal amount of chromosomes. ...
bam freebayes subset written 9 months ago by mernster0 • updated 9 months ago by ATpoint36k
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random selection of multi-sample vcf does not work
... Hey there, I am trying to randomly select variants from a multisample vcf file which I generated by merging several individual vcf files together using bcftools merge. This is the command that I am using: gatk SelectVariants -R /path/to/ref.fasta -V input.vcf -O output_1pct.vcf --select-ra ...
selectvariants gatk selectrandomfraction written 12 months ago by mernster0 • updated 12 months ago by finswimmer13k

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