User: bsmith030465

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bsmith030465150
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Posts by bsmith030465

<prev • 59 results • page 2 of 6 • next >
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PLINK: filter for indels
... Hi, How do I filter my plink files so that only indels are kept? I used the following command to keep only snps: plink --bfile myfile --snps-only --out myfile.snps Which command/option should I use to retain only indels? Thanks ...
plink written 14 months ago by bsmith030465150 • updated 14 months ago by zx87549.3k
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gnomAD: query utilitites
... Hi, I wanted to query the gnomAD database without having to download and configure the entire data. Is there a way gnomAD provides an API for programmatic access? For example, for a given variant id, I want to retrieve the Total 'Allele Count': INPUT: '1-978628-C-T' (or 'rs116586548') OUTP ...
gnomad written 14 months ago by bsmith030465150 • updated 14 months ago by Garan620
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PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
... Hi, I am trying to convert a vcf.gz file to bed/bim/fam format using PLINK2 (data is hg38). My command is: plink2 --vcf variants.vcf.gz --out variants --freq --make-bed --chr 1-22 XY I get an error: Error: Invalid chromosome code 'chr11_KI270721v1_random' on line 36088290 of How can I ...
vcf plink written 15 months ago by bsmith030465150 • updated 15 months ago by chrchang5237.1k
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Comment: C: samtools fastq compression
... file Sample_R1.fastq.gz Sample_R1.fastq.gz: gzip compressed data, from Unix, max speed ...
written 21 months ago by bsmith030465150
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samtools fastq compression
... I was trying to convert a cram file to two paired end fastq.gz files using the samtools command: samtools fastq -c -@2 -1 Sample_R1.fastq.gz -2 Sample_R2.fastq.gz Sample.cram I'm not sure if I am giving the right command for compression, since the .gz file is huge. Does this command look ok? ...
samtools fastq cram written 21 months ago by bsmith030465150
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Comment: C: bcftools: DP filter based on chromosome and sex
... Hi Pierre, Thanks!!! It would be extremely helpful if there was some documentation with this (where is it reading the male/female ids?). Also, what if I wanted to to do 'DP>10 & GQ >10', how do I incorporate multiple conditions? ...
written 22 months ago by bsmith030465150
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bcftools: DP filter based on chromosome and sex
... Hi, I want to filter my bcf file such that: 1. Autosomal chromosomes are filtered with DP > 20 2. X chromosome, for females is filtered with DP > 20 2. X chromosome, for males, with DP > 10 (i.e relax this criteria for males) My current plan is to split the data into autosomal (and chrY ...
wgs pyvcf bcftools samtools vcftools written 22 months ago by bsmith030465150 • updated 22 months ago by Pierre Lindenbaum129k
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Comment: C: bcftools filtering error
... So, according to the example, the -f flag would specify which columns to include, right? Shouldn't '-f PASS vcf_file.vcf' also include which column we want to apply the 'PASS' to? Sorry for the newbie questions! ...
written 23 months ago by bsmith030465150
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Comment: C: bcftools filtering error
... I was trying to replicate the manual : [bcftools filtering][1] Example in link: $ bcftools query -i'QUAL>20 && DP>10' -f'%CHROM %POS %QUAL %DP\n' file.bcf [1]: https://samtools.github.io/bcftools/howtos/filtering.html ...
written 23 months ago by bsmith030465150
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bcftools filtering error
... Hi, Apologies for the newbie question! I was trying to get some summary numbers from my vcf file. I wanted: 1. Summary numbers for all variants that PASS and are INDELS (per sample) 2. Summary numbers for all variants that PASS and are SNVs (per sample) I tried the command: bcftools query - ...
samtools next-gen bcftools written 23 months ago by bsmith030465150

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Popular Question 15 days ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
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