User: rbagnall
rbagnall • 1.6k
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Posts by rbagnall
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0
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Comment:
C: Figure out genotype from VCF line
... The last column shows the genotype
1/1:0,29:29:87:1131,87,0
the `1/1` means the genotype is `T/T`
a `0/0` would be `C/C`
a `0/1` would be `C/T`
the `0,29` means there were 0 reads with a C and 29 with a T
Have a look at the [VCF specifications][1] to understand the other columns
[1]: ht ...
3
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... Two things to help you:
> But what exactly does "T,<\non_ref>" mean in the ALT column?
You have only made a `g.vcf` file with `HaplotypeCaller`. This is a file that is 'poised' to be genotyped, but that has not yet been performed. You need to use the `g.vcf` file as input in the genotypi ...
written 12 days ago by
rbagnall • 1.6k
0
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... Can you get the reference genome to which your BAM file is aligned? I'm not sure how you could join together the sequence using only the example format from above. ...
written 19 days ago by
rbagnall • 1.6k
0
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... After `bedtools merge`, you could pipe the output into [bedtools getfasta][1]
[1]: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 19 days ago by
rbagnall • 1.6k
1
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1
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105
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... [VEP][1]. You will need the GRCh37 build for the shown variant
Put the genomic position in the 'input data' box, reformatted like so `16 20359634 20359634 C/G`
Make sure you select the 'exon and intron numbers' option. The variant will be in different exons, depending on the transcript.
[1]: h ...
written 22 days ago by
rbagnall • 1.6k
2
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1
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117
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Answer:
A: Does Splice AI use GRCh38?
... https://github.com/Illumina/SpliceAI
The answer lies within... ...
written 5 weeks ago by
rbagnall • 1.6k
0
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2
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136
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... and another that is a web based front end for GEMINI database
[https://academic.oup.com/bioinformatics/article/35/1/122/5047758][1]
[1]: https://academic.oup.com/bioinformatics/article/35/1/122/5047758 ...
written 7 weeks ago by
rbagnall • 1.6k
1
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141
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Comment:
C: Combining VCF files using GATK
... I would check which samples are missing, does this give you a clue? Perhaps the index is missing from the missing vcf files. Check which samples have been included:
zgrep -m 1 '^#CHROM' combine.g.vcf.gz | head -n 1 | cut -f 10- | tr '\t' '\n'
...
written 7 weeks ago by
rbagnall • 1.6k
1
vote
1
answer
118
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1
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... Sed command has `ILINNGPN_01481`
You are looking at `ILINNGPN_01482` in the before file ...
written 11 weeks ago by
rbagnall • 1.6k
2
votes
1
answer
165
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1
answers
... Lets look at a gene on the X chromosome, say [F8][1]
There is a variant at `X-154065843-G-A`, which is found in 103 males in the exome data and 92 males in the genome data, giving a total of 195 males who have this variant and are hemizygous.
Now lets get the male allele count (thus number of hemi ...
written 3 months ago by
rbagnall • 1.6k
Latest awards to rbagnall
Scholar
8 days ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
20 days ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
3 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Popular Question
5 months ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
Scholar
6 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
7 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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7 months ago,
created a comment with at least 3 up-votes.
For C: How to extract specific chromosome from vcf file
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21 months ago,
created 100 posts.
Good Answer
2.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Grep A Pattern From File
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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3.9 years ago,
created a comment with at least 3 up-votes.
For C: How to extract specific chromosome from vcf file
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4.1 years ago,
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4.2 years ago,
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For A: Trouble filtering CDS regions from Nextera Enrichment design
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