User: SteveL

gravatar for SteveL
SteveL80
Reputation:
80
Status:
Trusted
Location:
BCN
Last seen:
1 year, 4 months ago
Joined:
5 years, 10 months ago
Email:
s*************@gmail.com

about me

Posts by SteveL

<prev • 8 results • page 1 of 1 • next >
0
votes
2
answers
8.8k
views
2
answers
Comment: C: Checking kinship coefficients and relationships and comparing genotyping data to
... Hi Gael, Sorry for slow response but only just saw this. As far as I can tell it uses all SNPs you pass it. If you have a look in the paper, you can see where some of the limitations might be (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025716/#!po=61.3636). I am generally using multi-sample VCFs ...
written 16 months ago by SteveL80
5
votes
2
answers
8.8k
views
2
answers
Answer: A: Checking kinship coefficients and relationships and comparing genotyping data to
... Just to update, the --relatedness2 option to VCFTOOLS works nicely for pedigrees with WES data. This implements exactly the same algorithm used in KING. vcftools --gzvcf  YourZipped.vcf.gz  --relatedness2 First-degree relatives are ~0.25, and 2nd-degree ~0.125, and 3rd degree 0.0625. "Unrelated" ...
written 3.8 years ago by SteveL80
1
vote
6
answers
3.0k
views
6
answers
Answer: A: QUAL and AF GATK
... Yes, I would agree with using the 1000G phase.1 variants for filtering, and also keeping any positions that were not observed in the 1000G project, as these should be rare too. All the 1000G (phase 1) variants should be in dbSNP, but not the reverse, unless they removed some that they decided were ...
written 3.8 years ago by SteveL80
0
votes
6
answers
3.0k
views
6
answers
Answer: A: QUAL and AF GATK
... I am not that au fait with the 1000G calls to know why their first call is so far into Chr1. One thing to make sure of are that your calls were made on the same version of the genome. i.e. Version 37 not Version 38. Regardless, you should not expect ALL your calls to have been observed in the 1000G ...
written 3.8 years ago by SteveL80
1
vote
6
answers
3.0k
views
6
answers
Answer: A: QUAL and AF GATK
... Hi @Aleka, I had a longer answer, but lost it when I linked to follow the thread before posting, so briefly. A) GATK forum is the best place to ask, and search for answer to these questions. 1) You definitely want QUAL>30, and you will still have quite some false positives at the lower end 2) ...
written 3.8 years ago by SteveL80
1
vote
1
answer
2.5k
views
1
answers
Answer: A: Can ExAC database be used to filter out variant with MAF >1%?
... 1. I don't see why not - while there will be a few rare variants that may be enriched due to the datasets incorporated, they should still be very rare within the whole dataset. 2. I am not sure about this one, but I would guess they were the germ-line (i.e. non-cancer) samples, and can thus be rega ...
written 4.3 years ago by SteveL80
0
votes
2
answers
1.6k
views
2
answers
Answer: A: Genomes in a Bottle for GRCh38
... Not yet I don't believe, as they are still completing analyses on GRCh37 but they are putting together materials for GRCh37, so hopefully sometime in the next few months. ...
written 4.3 years ago by SteveL80
0
votes
5
answers
24k
views
5
answers
Comment: C: Human Exome Capture Library Coordinates Download
... Thanks, this worked well for me. ...
written 5.8 years ago by SteveL80

Latest awards to SteveL

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1544 users visited in the last hour