User: Tails

gravatar for Tails
Tails50
Reputation:
50
Status:
New User
Location:
New Zealand
Last seen:
1 day, 5 hours ago
Joined:
5 years, 1 month ago
Email:
t************@gmail.com

Posts by Tails

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Benchmarking small variant calls: TP, FP, TN, FN
... Interesting, I would curious to read what your critiques are. What other tools out there are good? I'm still looking at this problem months later. ...
written 1 day ago by Tails50
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Comment: C: Correct reference for Platinum Genomes?
... Yes I checked that out and used picard's reordersam command. But unfortunately, I get another error, which made me suspect that I'm not using the correct fasta file. One comment I found said that someone else experiencing this problem should reconsider their fasta file. Exception in thread "main" ht ...
written 10 days ago by Tails50
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Comment: C: Correct reference for Platinum Genomes?
... Thank you, do you mean from this link? ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/ucsc.hg19.fasta.gz Sorry for bothering you again, but I'm still getting this error message. Not sure if I should just start up another question thread? ##### ERROR MESSAGE: Input files reads and refer ...
written 11 days ago by Tails50
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Correct reference for Platinum Genomes?
... I'm trying to familiarize myself with haplotype caller by calling variants using the data supplied by platinum genomes. Here's the paper: [A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree][1] The BAM fi ...
genome bioinformatics sequencing written 11 days ago by Tails50 • updated 11 days ago by JC9.5k
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Can a command in RTG (or elsewhere) annotate the TP/TN/FP/FN's produced from RTG's vcfeval?
... I'm really liking RTG's vcfeval command, which takes in a gold standard vcf, a query vcf and a reference and outputs true positive vcf, true negative vcf, and the same for false positive, and false negative. My question is: is there some way to easily annotate the query vcf file so that each variant ...
genome sequence written 17 days ago by Tails50 • updated 6 days ago by Len Trigg1.4k
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Comment: C: Need help finding data from Google's DeepVariant paper
... Thanks for that. I looked and couldn't find the 50x bam file, there were other 300x bam files. Is it possible they only have the most up-to-date versions on there, are there archived versions? By the way, the second link doesn't work? ...
written 26 days ago by Tails50
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Need help finding data from Google's DeepVariant paper
... Apologies if this is not the usual type of question posted here. I'm a postgraduate student trying to understand Google's DeepVariant paper, and a step in the process is trying to run VQSR and seeing how it compares with DeepVariant. The authors have kindly provided their GATK code: https://static ...
genome snp sequencing written 27 days ago by Tails50
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Comment: C: How to filter GTF file and only print lines where the tag is a certain value?
... Oh sorry, it's also missing the condition: for each gene, meaning the if and else if should apply to each gene (for each unique string after the gene_name field), rather than each line. ...
written 6 months ago by Tails50
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Comment: C: How to filter GTF file and only print lines where the tag is a certain value?
... Thanks! That's almost exactly what I'm looking for, except even when I change the "print $13" at the end to "print $0", I still don't get the entire line, only the 9th column. Doing the cut -f9 so early in the process means you discarded the rest of the line, right? How do I get it to print the enti ...
written 6 months ago by Tails50
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Comment: C: How to filter GTF file and only print lines where the tag is a certain value?
... Oh yeah let's not forget grep. But I'm not sure how to make the condition if appris_principal doesn't exist in this line, check whether appris_candidate_longest exists. I neither, don't print. ...
written 6 months ago by Tails50

Latest awards to Tails

Great Question 4.5 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 4.5 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 4.5 years ago, created a question with more than 1,000 views. For How to get GQ after running BCFTools?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Beagle imputation output, incorrect genotype probability format?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Variant call format (VCF) file, how to get statistics per sample?
Student 4.5 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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