User: 4galaxy77

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4galaxy7790
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Posts by 4galaxy77

<prev • 35 results • page 1 of 4 • next >
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Answer: A: How Can I Count Snps In My Final Vcf Files
... If all your variants in the vcf are SNPS, then a very quick way is to first index and then index again with the -n flag. bcftools index data.vcf bcftools index -n data.vcf ...
written 1 day ago by 4galaxy7790
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Comment: C: Principle component analysis using VCF file as input.
... The important error here is "Error: data.bim cannot contain multiallelic variants". ...
written 2 days ago by 4galaxy7790
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Comment: C: Is it possible to run haplotypecaller in gnu parallel ?
... Something like this should work find . -name '*.bam' | rev | cut -c4- | parallel -I{} gatk --java-options "-Xmx40g" HaplotypeCaller \ -R /media/gatk/Homo_sapiens_assembly38.fasta \ -I {}.bam \ -O {}.vcf.gz \ --dbsnp /media/gatk/dbsnp_138.hg38.vcf.gz \ -L /media/gatk/tar ...
written 3 days ago by 4galaxy7790
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Answer: A: Principle component analysis using VCF file as input.
... I would reccomend first converting to plink format (I have found a couple of odd things happening when you use a vcf directly). plink2 --vcf data.vcf --make-bed --out data If you haven't already, it's a good thing to LD prune and remove rare variants plink2 --bfile data --maf 0.01 --indep ...
written 3 days ago by 4galaxy7790
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Comment: C: Mutating columns by changing units - R/dplyr solution
... To share your data, please paste in the results of ``dput(head(data))`` into your original question. Thanks. ...
written 5 days ago by 4galaxy7790
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Comment: C: SHAPEIT4 incorrect number of columns
... How did you convert it to .vcf and the bgz format? also, can you post a sample of the header and the first non-header line of the .vcf? ...
written 8 days ago by 4galaxy7790
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Comment: C: Shape IT Phasing on Windows
... What's your sample size and number of SNPs like? I presume (although correct me if I'm wrong) that you are planning to run it on your local PC or laptop? This could take a very long time if you have more than a few samples and SNPs and chromosomes to run. If it's possible, I would recommend trying t ...
written 9 days ago by 4galaxy7790
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Answer: A: How to convert a VCF with genotypes and phasing info to list of haplotypes for R
... Could try using plink to convert to Oxford haps format https://www.cog-genomics.org/plink/2.0/formats#haps - it more or less looks like what you need. unsure exactly how accurate the haplotype calling from GATK is from short reads. If you need accurate haplotypes across the whole genome, it might b ...
written 9 days ago by 4galaxy7790
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Answer: A: variant filtering based on high quality reference - removing false positives
... Download the high quality reference and then print out all the SNPs. bcftools view -v snps reference.vcf | bcftools query -f'%CHROM\t%POS\n' > reference_positions.txt Then extract these positions from the target vcf. bcftools view -T reference_positions.txt target.vcf > target_filt ...
written 9 days ago by 4galaxy7790
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automatically create index files from output in bcftools
... say i am running a command in bcftools like /share/apps/genomics/bcftools-1.9/bin/bcftools view -O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz -R $variants --exclude-types indels $sample Rather than then having to run a separate command on the output file to produce an index file: ...
software error written 23 months ago by 4galaxy7790 • updated 23 months ago by Kevin Blighe69k

Latest awards to 4galaxy77

Popular Question 22 months ago, created a question with more than 1,000 views. For 0 mapping hits for blast2go
Popular Question 22 months ago, created a question with more than 1,000 views. For .gtf file error in Tophat2 - Error at parsing .tlst line (invalid strand):
Popular Question 22 months ago, created a question with more than 1,000 views. For Minimum number of replicates for gene co-expression analysis
Popular Question 22 months ago, created a question with more than 1,000 views. For Measuring transcriptional noise
Scholar 22 months ago, created an answer that has been accepted. For C: filtering by POS in bcftools
Popular Question 22 months ago, created a question with more than 1,000 views. For 0 mapping hits for blast2go
Popular Question 3.6 years ago, created a question with more than 1,000 views. For 0 mapping hits for blast2go
Popular Question 3.6 years ago, created a question with more than 1,000 views. For .gtf file error in Tophat2 - Error at parsing .tlst line (invalid strand):
Popular Question 3.6 years ago, created a question with more than 1,000 views. For fastq_quality_filter: input file (-) has unknown file format (not FASTA or FASTQ)
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Best primer design software
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Minimum number of replicates for gene co-expression analysis

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