User: Shane McCarthy

gravatar for Shane McCarthy
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Cambridge, Cambridgeshire
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1 year, 6 months ago
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Posts by Shane McCarthy

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Filtering VCF file by INFO flag
... bcftools view -i 'CGA_XR ~"dbsnp"' file.vcf ...
written 2.4 years ago by Shane McCarthy320
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Job: Genomics Data Scientist - Sanger Institute, Cambridge, UK
... **The Vertebrate Resequencing team at the Wellcome Trust Sanger Institute is looking to recruit a motivated Genomics Data Scientist**. The Vertebrate Resequencing (http://www.sanger.ac.uk/science/groups/vertebrate-resequencing) team at the Wellcome Trust Sanger Institute is seeking a motivated geno ...
genome assembly job written 3.1 years ago by Shane McCarthy320
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Answer: A: getting GQ values with VCF using SAMTOOLS Mpileup
... Add `-f GQ` to the `bcftools call` command. ...
written 3.3 years ago by Shane McCarthy320
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Comment: C: samtools mpileup VCF output
... Because bcftools call is actually doing the variant calling. mpileup is only outputting genotype likelihoods (in VCF or BCF format), which are then used by bcftools to call variants (in VCF of BCF format). Does that make sense? ...
written 3.3 years ago by Shane McCarthy320
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Answer: A: BCF file is too big? (from 3,73 GB sorted.bam file to over 200 GB BCF)
... The -u flag means you are writing out uncompressed BCF. Use -g instead to write out compressed BCF. ...
written 3.3 years ago by Shane McCarthy320
1
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Answer: A: 1000 genomes project mitochondrial DNA sequences
... As it says in that README the fasta file is located here: ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/release/20130502/supporting/MT/chrMT_sequences_2534.20160101.fasta.gz ...
written 3.4 years ago by Shane McCarthy320
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Answer: A: samtools mpileup - how to extract the alternative allele counts for *each* alter
... You'll need to update to the latest samtools/bcftools (1.3) and then there are new mpileup tag (-t) options -- AD, ADF, ADR which will give per-allele depth (AD) per-allele depth on the forward (ADF) and reverse (ADR) strands. ...
written 3.5 years ago by Shane McCarthy320
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Comment: C: VCF to genotype file of specific format
... Then replace the tr command at the end with tr "/|" " " ...
written 3.5 years ago by Shane McCarthy320
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Answer: A: VCF to genotype file of specific format
... For REF and ALT in the last two columns: bcftools query -f '%ID %CHROM %POS %REF %ALT\n' input.vcf For the actual alleles of the individual in the last two columns: bcftools query -f '%ID %CHROM %POS[ %TGT]\n' input.vcf | tr "/" " " ...
written 3.5 years ago by Shane McCarthy320
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Answer: A: BCFTools view equivelent of GATK -T SelectVariants -sn sample_x --excludeNonVari
... How about bcftools view -c1 input.vcf to select sites with at least one non-ref allele? ...
written 3.9 years ago by Shane McCarthy320

Latest awards to Shane McCarthy

Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: VCF to genotype file of specific format
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: samtools mpileup VCF output
Scholar 3.4 years ago, created an answer that has been accepted. For A: BCFTools view equivelent of GATK -T SelectVariants -sn sample_x --excludeNonVari
Scholar 3.5 years ago, created an answer that has been accepted. For A: BCFTools view equivelent of GATK -T SelectVariants -sn sample_x --excludeNonVari
Scholar 3.5 years ago, created an answer that has been accepted. For A: BCFTools view equivelent of GATK -T SelectVariants -sn sample_x --excludeNonVari
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: A tool to annotate one VCF file with INFO records of another VCF taking SNP into
Scholar 3.9 years ago, created an answer that has been accepted. For A: A tool to annotate one VCF file with INFO records of another VCF taking SNP into
Scholar 4.3 years ago, created an answer that has been accepted. For A: A tool to annotate one VCF file with INFO records of another VCF taking SNP into
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: A tool to annotate one VCF file with INFO records of another VCF taking SNP into

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