User: rbagnall

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Posts by rbagnall

<prev • 123 results • page 1 of 13 • next >
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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 ...
written 8 days ago by rbagnall1.6k • updated 8 days ago by RamRS27k
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Answer: A: Figure out genotype from VCF line
... 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 rbagnall1.6k
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Comment: C: combining / merging overlapping reads in bam file to one in silico long read
... 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 rbagnall1.6k
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Answer: A: combining / merging overlapping reads in bam file to one in silico long read
... 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 rbagnall1.6k
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Answer: A: determine exon number from variant genomic coordinates
... [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 rbagnall1.6k
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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 rbagnall1.6k
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Comment: C: What's the best way to serve VCF data on web?
... 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 rbagnall1.6k
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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 rbagnall1.6k
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Answer: C: Problem using SED for change IDs in gff file
... Sed command has `ILINNGPN_01481` You are looking at `ILINNGPN_01482` in the before file ...
written 11 weeks ago by rbagnall1.6k
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Answer: A: GNOMAD exome vcf field missing? number of hemizygous individuals
... 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 rbagnall1.6k

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Scholar 8 days ago, created an answer that has been accepted. For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
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
Commentator 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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Scholar 2.8 years ago, created an answer that has been accepted. For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Commentator 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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