User: bsmith030465

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bsmith030465120
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Posts by bsmith030465

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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 3 months ago by bsmith030465120
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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 3 months ago by bsmith030465120
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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 4 months ago by bsmith030465120
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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 4 months ago by bsmith030465120 • updated 4 months ago by Pierre Lindenbaum116k
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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 5 months ago by bsmith030465120
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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 5 months ago by bsmith030465120
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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 5 months ago by bsmith030465120
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plink: vcf to ped
... Hi, I wanted to convert a vcf file to ped/map format. I looked at the archived posts, but the command doesn't seem to give the ped file. I have tried both with plink v 1.9 & plink2, and my commands are: plink --vcf genomeDF.vcf.gz --freq --maf 0.05 --chr 1-22 --recode --out genomeDF.vcf.g ...
plink snp sequencing written 9 months ago by bsmith030465120 • updated 9 months ago by chrchang5234.3k
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Rsamtools: error with quickBamFlagSummary
... Hi, I was trying to determine if my bam file was single or pair ended. However, when I try to use Rsamtools, I get an error: > quickBamFlagSummary(file="/Users/bsmith/Documents/run_s1_Aligned_Reads.bam") Error: identical(length(N_1seg_rec_per_uqname) + length(N_mseg_rec_per_uqname), .. ...
rsamtools rna-seq written 13 months ago by bsmith030465120
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Comment: C: Adjust for covariates
... Thanks for the reply!! I think this might do it! ...
written 13 months ago by bsmith030465120

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