User: biogirl

gravatar for biogirl
biogirl150
Reputation:
150
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Location:
European Union
Last seen:
2 months ago
Joined:
4 years, 7 months ago
Email:
j*************@imperial.ac.uk

Posts by biogirl

<prev • 52 results • page 1 of 6 • next >
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Comment: C: vcftools vcf-merge error
... I think I've sorted it - I've just grepped out any of the offending characters in the GT field. ...
written 9 weeks ago by biogirl150
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Comment: C: vcftools vcf-merge error
... `##FORMAT=` ...
written 9 weeks ago by biogirl150
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Comment: C: vcftools vcf-merge error
... It seems there are a couple of offending positions in each file (96 of them). Is there any way to force through these positions, or do I remove them? ...
written 9 weeks ago by biogirl150
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Comment: C: vcftools vcf-merge error
... Yes, everything has been gzipped and tab indexed. I've noticed I also get an error when using GATK CombineVariants about the VCFs. These were generated using GATK HaplotypeCaller. Never had this issue before, nothing has changed in the pipeline - the only difference is the source of the data (HiSeq ...
written 9 weeks ago by biogirl150
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Comment: C: vcftools vcf-merge error
... Hi - I did not know that! Thanks! Ok, I've tried bcftools but still get a segmentation fault: [E::vcf_parse_format] Invalid character 'f' in 'GT' FORMAT field I'm assuming this isn't a vcftools/bcftools issue? ...
written 9 weeks ago by biogirl150
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vcftools vcf-merge error
... Hi, I've never had this problem before using vcftools v0.1.12 vcf-merge, but now it throws up this error: Could not parse gtype string [fail] .. VIII:214 WGS at /apps/vcftools/0.1.12/lib/perl5/site_perl/Vcf.pm line 172, <__ANONIO__> line 2. Vcf::throw('Vcf4_2=HASH(0x1bc4b2 ...
vcf-merge vcftools written 9 weeks ago by biogirl150
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Masking repeats in your alignment
... Hi, I've been looking at a number of posts about repeat masking here on biostars, but some of the topics are a number of years old so I was wondering what the general consensus of thinking was on repeat masking in your pipeline to align reads to a reference genome and call SNPs. There's this post ...
genome repeats sequencing written 19 months ago by biogirl150 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: Linkage disequilibrium decay sanity check
... Amazing answer, thank you! ...
written 22 months ago by biogirl150
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Linkage disequilibrium decay sanity check
... Hi guys, I'm looking at linkage disequilibrium using r2 statistic from Plink, and just basically want to run by two things: 1) A sanity check for what I've run in plink 2) Looking at R code to plot r2 over distance For plink, I used an ld-window-kb size of 1 (so 1000 bp) and removed the default l ...
linkage disequilibrium plink snp written 2.0 years ago by biogirl150 • updated 22 months ago by willgilks250
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Comment: C: Analysis past the differentially expressed genes: RNAseq
... Thanks for these suggestions - IncRNA is something I really hadn't considered, and definitely falls in the 'cooler' category! ...
written 3.2 years ago by biogirl150

Latest awards to biogirl

Great Question 18 months ago, created a question with more than 5,000 views. For SNPs only output from bcftools
Popular Question 18 months ago, created a question with more than 1,000 views. For Analysis past the differentially expressed genes: RNAseq
Popular Question 18 months ago, created a question with more than 1,000 views. For PLINK error locus has more than 2 alleles
Popular Question 18 months ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Popular Question 18 months ago, created a question with more than 1,000 views. For ddRADseq and segregating SNPs
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Arabidopsis GFF files
Popular Question 19 months ago, created a question with more than 1,000 views. For PLINK error locus has more than 2 alleles
Student 21 months ago, asked a question with at least 3 up-votes. For PSMC using haploid genomes
Popular Question 23 months ago, created a question with more than 1,000 views. For PLINK error locus has more than 2 alleles
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Binary SNP matrix into APE (R)
Popular Question 3.1 years ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Popular Question 3.2 years ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Popular Question 3.5 years ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Supporter 3.8 years ago, voted at least 25 times.

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