User: bsmith030465

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bsmith030465140
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Posts by bsmith030465

<prev • 48 results • page 1 of 5 • next >
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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 4 days ago by bsmith030465140 • updated 4 days ago by chrchang5234.8k
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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 5 months ago by bsmith030465140
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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 5 months ago by bsmith030465140
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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 6 months ago by bsmith030465140
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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 6 months ago by bsmith030465140 • updated 6 months ago by Pierre Lindenbaum117k
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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 7 months ago by bsmith030465140
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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 7 months ago by bsmith030465140
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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 7 months ago by bsmith030465140
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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 11 months ago by bsmith030465140 • updated 11 months ago by chrchang5234.8k
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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 15 months ago by bsmith030465140

Latest awards to bsmith030465

Great Question 4 months ago, created a question with more than 5,000 views. For PLINK: merge .bed files
Epic Question 4 months ago, created a question with more than 10,000 views. For PLINK: merge .bed files
Popular Question 4 months ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 11 months ago, created a question with more than 1,000 views. For PLINK: Change affection status
Popular Question 15 months ago, created a question with more than 1,000 views. For GRanges intersect operation
Great Question 22 months ago, created a question with more than 5,000 views. For PLINK: merge .bed files
Popular Question 22 months ago, created a question with more than 1,000 views. For GRanges intersect operation
Popular Question 22 months ago, created a question with more than 1,000 views. For PLINK: Change affection status
Popular Question 22 months ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 22 months ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
Popular Question 23 months ago, created a question with more than 1,000 views. For PLINK: Change affection status
Great Question 2.3 years ago, created a question with more than 5,000 views. For How To Determine The Statistical Significance Of Overlap (Intersect) Between Three Sets
Popular Question 2.3 years ago, created a question with more than 1,000 views. For PLINK: Change affection status
Popular Question 2.3 years ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 2.6 years ago, created a question with more than 1,000 views. For PLINK format to EIGENSTRAT format
Popular Question 3.7 years ago, created a question with more than 1,000 views. For PLINK format to EIGENSTRAT format
Popular Question 3.7 years ago, created a question with more than 1,000 views. For PLINK: Convert bed,bim, fam to vcf file
Student 6.0 years ago, asked a question with at least 3 up-votes. For How To Determine The Statistical Significance Of Overlap (Intersect) Between Three Sets

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