User: fwuffy
fwuffy • 100
- Reputation:
- 100
- Status:
- Trusted
- Location:
- Michigan, USA
- Website:
- http://glyphdataservic...
- Last seen:
- 3 months, 2 weeks ago
- Joined:
- 5 years, 7 months ago
- Email:
- p******@gmail.com
Software developer working in NGS analytics.
Posts by fwuffy
<prev
• 29 results •
page 1 of 3 •
next >
0
votes
2
answers
4.7k
views
2
answers
... This fails on RefSeq GTFs from NCBI.
You may also need to set the delimiter and sort on end position. I've had better luck with the -V sort (natural version sort) algo on chromosome names, but I think that is a matter of personal preference, whether you want alt contigs interleaved with primary c ...
written 4 months ago by
fwuffy • 100
0
votes
0
answers
235
views
0
answers
... It seems to be running fine without having built the reference db with separate fasta files with protein sequence and CDS. The build process can accept those, but I just built the db with genomic dna FASTA.
The GFF and GTF I used have CDS data and some protein annotations, but not the translated ...
written 4 months ago by
fwuffy • 100
1
vote
0
answers
235
views
0
answers
... I'm working on building a snpEff db for GRCh38 patch 13 RefSeq assembly. The latest pre-built snpEff db available for RefSeq is patch 7. I need p13 for consistency within pipelines. (don't ask me why patch 13 isn't available in the pre-built snpEff library. They recommend using Ensembl not RefSeq) ...
written 4 months ago by
fwuffy • 100
12
votes
2
answers
575
views
7 follow
2
answers
... Does anyone know if BWA Mem -M flag (mark shorter split hits as secondary) will have a detrimental effect on structural variation calling using split reads with Delly?
I orignially added it to my BWA mapping pipeline for compatibility with Picard/GATK but I believe that issue has been resolved in ...
0
votes
2
answers
696
views
2
answers
... Ok, thanks. I'll try that... ...
written 22 months ago by
fwuffy • 100
5
votes
2
answers
696
views
2
answers
... Hi- I need a reliable method to identify SNPs in the human genome with the most variability. Does anyone know of a data file I can download (a VCF or something easy to parse) that contains snps and a conservation score like PhyloP or PhastCons?
In lieu of that if you can recommend something to iden ...
written 22 months ago by
fwuffy • 100
• updated
22 months ago by
colindaven • 2.5k
2
votes
0
answers
2.2k
views
0
answers
... I know there are some good homozygous calls in this VCF, yet vcf-tools can not see them for whatever reason. Any filtering for MAF or alt read count results in total elimination of all 1/1 homozygous calls.
an example VCF row:
chr3 69313555 rs1483895 C T 222 . AC1=2;AC=4;AF1=1;AN=4;ANN=T|i ...
written 2.7 years ago by
fwuffy • 100
0
votes
0
answers
1.4k
views
0
answers
... Here's a variant SNP with raw depth of 2, and DP4 field shows 1 alt-forward read.
Can someone help me understand why this is called homozygous 1/1 at this position intead of hetero 0/1?
(I am filtering out calls with DP < 5 after this, but it still raises questions)
Thanks!
samtools mpil ...
written 2.7 years ago by
fwuffy • 100
0
votes
1
answer
1.5k
views
1
answers
Comment:
C: Picard MarkDuplicates fatal error
... Updating to 2.17 fixed it
Thanks! ...
written 2.7 years ago by
fwuffy • 100
0
votes
1
answer
1.5k
views
1
answers
Comment:
C: Picard MarkDuplicates fatal error
... Using 1.119
Yes Googled but ran into a different error, but this looks like it. Thanks, I will try the upgrade. ...
written 2.7 years ago by
fwuffy • 100
Latest awards to fwuffy
Great Question
5 months ago,
created a question with more than 5,000 views.
For Samtools mpileup quality scores all zero
Popular Question
10 months ago,
created a question with more than 1,000 views.
For SnpSift annotate reporting extra alleles not present in the input VCF
Popular Question
12 months ago,
created a question with more than 1,000 views.
For SnpSift annotate reporting extra alleles not present in the input VCF
Student
12 months ago,
asked a question with at least 3 up-votes.
For BWA Mem -M flag (mark split hits) effect on structural variation calling
Popular Question
17 months ago,
created a question with more than 1,000 views.
For SnpSift annotate reporting extra alleles not present in the input VCF
Supporter
22 months ago,
voted at least 25 times.
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For SnpSift annotate reporting extra alleles not present in the input VCF
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Convert VCF to BCF
Popular Question
4.9 years ago,
created a question with more than 1,000 views.
For Convert VCF to BCF
Popular Question
4.9 years ago,
created a question with more than 1,000 views.
For Samtools mpileup quality scores all zero
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1506 users visited in the last hour