User: Tails

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Tails30
Reputation:
30
Status:
New User
Location:
New Zealand
Last seen:
6 days ago
Joined:
4 years, 4 months ago
Email:
t************@gmail.com

Posts by Tails

<prev • 7 results • page 1 of 1 • next >
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Benchmarking small variant calls: TP, FP, TN, FN
... I'm reading [this excellent paper][1] which describes a methodology to standardize variant benchmarking process. They say that the normal binary classification form (i.e., TP, FP, FN, and statistics derived from these) are not simple for variant calls. So they go on to describe how they do this, in ...
genome snp sequencing written 6 days ago by Tails30 • updated 6 days ago by WouterDeCoster39k
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Best resources for understanding GATK best practices pipeline (or similar)
... I've been trying to find a resource for understanding the various steps in the GATK pipeline or more generally, mapping and alignment, and variant calling in general. There seems to be a huge learning curve involved and every resource I've come across assumes you've worked with the data for quite a ...
genome assembly sequence snp alignment written 17 days ago by Tails30 • updated 16 days ago by Kevin Blighe42k
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How to extract entire info column from VCF file using bcftools
... I want to extract the whole info column, and the documentation indicates that %INFO should extract the whole info column. https://samtools.github.io/bcftools/bcftools.html#query I've tried the following: bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO[\t%SAMPLE=%AD]\n' file.vcf But I get ...
software error bcftools snp written 4 weeks ago by Tails30 • updated 4 weeks ago by finswimmer11k
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Variant call format (VCF) file, how to get statistics per sample?
... It is quite common to find tools that report on statistics per variant/marker, given a vcf file, but does anyone know of a tool that can report on stats per sample? More specifically, I am looking for a tool that can tell me the proportion of variants/markers that are heterozygous (1/0 or 0/1) for ...
vcf myposts written 3.8 years ago by Tails30 • updated 13 months ago by ruth_s0
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Beagle imputation output, incorrect genotype probability format?
... After imputing with BEAGLE one of the markers (a deletion) doesn't have three genotype probabilities but instead just has a '1' written in its place.. usually there are three comma separated probabilities.. does anyone know if this is a bug in BEAGLE? ##INFO=<ID=AR2,Number=1,Type=Float,Descripti ...
sequence imputation beagle written 4.0 years ago by Tails30
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Missing -d option in new BCFTools?
... In the old version of BCFTools (0.1.19), there was an option "-d skip loci where less than FLOAT fraction of samples covered [0]" It seems to have disappeared in the new version (1.1). Is there an alternative that does the same thing? Thanks! :-) ...
sequence snp written 4.4 years ago by Tails30 • updated 4.4 years ago by RamRS21k
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How to get GQ after running BCFTools?
... New version of BCFTools (using call instead of view) doesn't produce VCF files with GQs in the FORMAT field. Does anyone know how to get it in the new version (1.1)? ...
snp sequencing written 4.4 years ago by Tails30 • updated 4.2 years ago by timothee.cezard40

Latest awards to Tails

Great Question 3.8 years ago, created a question with more than 5,000 views. For Variant call format (VCF) file, how to get statistics per sample?
Epic Question 3.8 years ago, created a question with more than 10,000 views. For Variant call format (VCF) file, how to get statistics per sample?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How to get GQ after running BCFTools?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Beagle imputation output, incorrect genotype probability format?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Variant call format (VCF) file, how to get statistics per sample?
Student 3.8 years ago, asked a question with at least 3 up-votes. For Variant call format (VCF) file, how to get statistics per sample?

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