User: rbagnall
rbagnall • 1.3k
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Posts by rbagnall
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0
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... Have a look at [PLINK/SEQ][1] tutorials. They give a walk through of the steps involved in exploring variation in vcf files, including different types of association tests.
You should probably start at the PLINK/SEQ_101 and the extended tutorial, which have lots of informative steps on setting up t ...
written 3 months ago by
rbagnall • 1.3k
3
votes
3
answers
333
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3
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... Yes.
1. The Sanger sequencing trace will look very 'clean', with only single allele peaks on the chromatogram at each nucleotide (see the first 8 nucleotides of ATpoint's figure above), but there will be some additional bases compared to the reference at the site of the insertion.
Some other point ...
written 3 months ago by
rbagnall • 1.3k
0
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0
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315
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... Do the chromosome names in hs37d5 look like 1, 2, 3 etc, and in GRCh38 look like chr1, chr2, chr3? ...
written 4 months ago by
rbagnall • 1.3k
1
vote
1
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321
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1
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... hmm, try
= "Pathogenic"
rather than
~ "Pathogenic" ...
written 4 months ago by
rbagnall • 1.3k
1
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1
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321
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1
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... The clinvar.vcf needs to be bgzip compressed and tabix indexed first.
uncompress then bgzip
gunzip grch37_clinvar.vcf.gz | bgzip > grch37_clinvar.bgzip.vcf.gz
tabix index
tabix -p vcf grch37_clinvar.bgzip.vcf.gz
view alleles in grch37_clinvar.bgzip.vcf.gz that have pathogenic in the CLNSI ...
written 4 months ago by
rbagnall • 1.3k
3
votes
1
answer
321
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1
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... You can download clinvar as a vcf, aligned to GRCh37 or GRCh38 from [here][1]
The vcf INFO column contains the clinvar allele id (ALLELEID) and clinical significance, e.g. CLNSIG=Benign, CLNSIG=Pathogenic, so you could load both in IGV, or compare your vcf with the clinvar vcf for similar alleles u ...
written 4 months ago by
rbagnall • 1.3k
1
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1
answer
345
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1
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... Thanks Emily, that worked!
For those that are interested, I got the gff file from here:
ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gff.gz
Then unzipped, sorted, bgzipped and tabix indexed, as described on the VEP link provided ...
written 5 months ago by
rbagnall • 1.3k
2
votes
1
answer
345
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1
answer
... Hi,
I'm using the most current version of VEP (Ensembl variant effect predictor v92.3) and annotating against the RefSeq transcripts. The output shows that it is using
`refseq version 01_2015`
How can I update this to a more recent release? I can't seem to find where the refseq database has bee ...
written 5 months ago by
rbagnall • 1.3k
• updated
5 months ago by
Emily_Ensembl ♦ 16k
0
votes
1
answer
332
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1
answers
... Not really the right place for this question.
It's best to sort this out way before submission. When you submitted the review, who did you list as authors, and which institution did you list as your affiliation?
...
written 6 months ago by
rbagnall • 1.3k
1
vote
2
answers
332
views
2
answers
Answer:
A: gnomad_AF from VEP is NA
... It may depend on the ethnicity of the sample(s). An Australian Indigenous person will show many apparently novel variants, although most will be ethnic specific and this population is not represented in GnomAD. In this case, the variants are absent from GnomAD, but not necessarily 'rare' in the Aust ...
written 7 months ago by
rbagnall • 1.3k
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For A: Grep A Pattern From File
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For LOD score of a single genotype
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For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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For C: How to extract specific chromosome from vcf file
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For A: Trouble filtering CDS regions from Nextera Enrichment design
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For Free HiSeq X Ten human genome fastq test data
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