User: Matt Miossec
Matt Miossec • 350
- Reputation:
- 350
- Status:
- Trusted
- Location:
- UK/Oxford/Wellcome Centre for human genetics
- Twitter:
- @RealMattJM
- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 8 years, 5 months ago
- Email:
- m**********@gmail.com
I am a French/American bioinformatics researcher. My doctoral thesis was in the field of Human Genetics and was conducted in the UK. Worked in Chile for close to 4 years at the centre for bioinformatics and integrative biology for 3 years. Now work at the Wellcome Centre for human genetics in Oxford.
Posts by Matt Miossec
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... The most likely explanation is that the file you're using to define contig ploidy priors has 7 columns instead of 5 in one or more of its rows. Even if it looks like that is not the case, double check you don't have any extra tabs (you can check with vim on the command line or notepad++). Hope this ...
written 10 months ago by
Matt Miossec • 350
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... GATK4 germlineCNVcaller is available now. It'd be great to see how it stacks up against some of the older methods out there. ...
written 11 months ago by
Matt Miossec • 350
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... Yes, this appears to be normal for the moment, I imagine it will probably change as the tool is further developed.
The information you're looking for is in the last column. The first element in that column, GT, stands for the call of expected ploidy (0), deletion (1) and duplication (2):
The follo ...
written 16 months ago by
Matt Miossec • 350
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Comment:
C: Locus in my snps.vcf file
... That is true, my mistake. ...
written 4.6 years ago by
Matt Miossec • 350
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Answer:
A: Locus in my snps.vcf file
... Submit your VCF file to ANNOVAR, it will provide all the annotation you need:
http://wannovar.usc.edu/ ...
written 4.6 years ago by
Matt Miossec • 350
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Comment:
C: Large VCF QUAL Values
... Yes, it's definitely the read depth. I didn't even know that depth of sequencing was possible. ...
written 4.6 years ago by
Matt Miossec • 350
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Comment:
C: VCF file without SNPs
... I think you need to address this first error in order to get output. First, can you check your BAM file isn't truncated using SAMtools view? Second, can you make sure that the FASTA file you're using for variant calling is exactly the same you used for alignment? ...
written 4.6 years ago by
Matt Miossec • 350
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... When you copy either the end of your input or the full input, you're also copying the newline character. Before printing your string, apply `rstrip()`. That should fix it. ...
written 4.6 years ago by
Matt Miossec • 350
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... I've updated the AWK command to take that into account. The awk commands interprets '[^R]' as "any term that isn't R". So if ':F' is at the end of the field, it will not exclude it because it is expecting a term that isn't there. I have fixed this issue by writing '[^R]*$' instead. The asterix stand ...
written 4.7 years ago by
Matt Miossec • 350
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... You could use a simple AWK command (assuming the INFO column is the 8th column):
`awk '$8!~/:R/ && $8!~/:F[^R]*$/` FILE.vcf > FILE_updated.vcf
Removes all lines with either :R or :F (unless :FR)
If you want to do it for all your VCF files:
for file in `ls *.vcf`; do **awk comm ...
written 4.7 years ago by
Matt Miossec • 350
Latest awards to Matt Miossec
Popular Question
4.1 years ago,
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For Does Samtools Tview Hide Pcr And Optical Duplicates?
Voter
4.6 years ago,
voted more than 100 times.
Teacher
4.7 years ago,
created an answer with at least 3 up-votes.
For A: Rare Variant Snps With No Allele Frequency
Popular Question
4.8 years ago,
created a question with more than 1,000 views.
For Does Samtools Tview Hide Pcr And Optical Duplicates?
Popular Question
5.9 years ago,
created a question with more than 1,000 views.
For Does Anybody Know Which Gatk Walkers Are Positively Affected By Pedigree Information?
Supporter
6.8 years ago,
voted at least 25 times.
Teacher
6.8 years ago,
created an answer with at least 3 up-votes.
For A: Rare Variant Snps With No Allele Frequency
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6.8 years ago,
asked a question with at least 3 up-votes.
For How Large Can A Coverage Discrepancy Be Between Two Aligners, Specifically Bwa And Novoalign
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