User: fwuffy
fwuffy • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- Michigan, USA
- Website:
- http://glyphdataservic...
- Last seen:
- 1 month ago
- Joined:
- 4 years, 8 months ago
- Email:
- p******@gmail.com
Software developer working in NGS analytics.
Posts by fwuffy
<prev
• 26 results •
page 1 of 3 •
next >
10
votes
2
answers
133
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
505
views
2
answers
... Ok, thanks. I'll try that... ...
written 11 months ago by
fwuffy • 90
5
votes
2
answers
505
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 11 months ago by
fwuffy • 90
• updated
11 months ago by
colindaven • 1.9k
2
votes
0
answers
1.3k
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 21 months ago by
fwuffy • 90
0
votes
0
answers
853
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 21 months ago by
fwuffy • 90
0
votes
1
answer
996
views
1
answers
Comment:
C: Picard MarkDuplicates fatal error
... Updating to 2.17 fixed it
Thanks! ...
written 21 months ago by
fwuffy • 90
0
votes
1
answer
996
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 21 months ago by
fwuffy • 90
4
votes
1
answer
996
views
1
answer
... Hi, I'm running Picard MarkDuplicates on a sorted mapped BAM file. It's mapped with bwa mem, sorted with samtools sort. Pretty standard.
I'm running it from a cron job. The process seems to run almost to completion and generates a bam slightly larger than the input.
This is genomic data, an exo ...
0
votes
1
answer
793
views
1
answers
Comment:
C: VCF PL Values not making sense
... Oh right!!! Duh. It's been a while...
so I'd have
A/A:72,
A/B:25,
A/C:45,
A/D: 27,
B/B: 0,
B/C: 47,
B/D: 40,
C/C: 13,
C/D: 15,
D/D: 59
The coverage is low cause it's a sub-sampled fastq. I also know there are issues around indels but just for t ...
written 22 months ago by
fwuffy • 90
2
votes
1
answer
793
views
1
answer
... Hi- Can someone help me identify these PL (phred likelihood) genotype values for this multi-allelic indel row in a VCF?
The VCF row:
chr1 36418926 . caagaaa cAAAAaagaaa,caa,cAAaagaaa 9.95049 . INDEL;IDV=4;IMF=0.666667;DP=6;VDB=0.0340507;SGB=-0.556411;MQSB=1;MQ0F=0;AF1=0.502508;AC1=1;DP4=1,0,3 ...
written 22 months ago by
fwuffy • 90
Latest awards to fwuffy
Student
4 weeks 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
6 months ago,
created a question with more than 1,000 views.
For SnpSift annotate reporting extra alleles not present in the input VCF
Supporter
11 months ago,
voted at least 25 times.
Popular Question
2.2 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
2.2 years ago,
created a question with more than 1,000 views.
For Convert VCF to BCF
Popular Question
3.9 years ago,
created a question with more than 1,000 views.
For Convert VCF to BCF
Popular Question
3.9 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: 1497 users visited in the last hour