User: fwuffy
fwuffy • 50
- Reputation:
- 50
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- Trusted
- Location:
- Michigan, USA
- Website:
- http://glyphdataservic...
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 4 years ago
- Email:
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Software developer working in NGS analytics.
Posts by fwuffy
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... Ok, thanks. I'll try that... ...
written 3 months ago by
fwuffy • 50
5
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... 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 3 months ago by
fwuffy • 50
• updated
3 months ago by
colindaven • 1.2k
2
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... 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 13 months ago by
fwuffy • 50
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... 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 13 months ago by
fwuffy • 50
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1
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616
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Comment:
C: Picard MarkDuplicates fatal error
... Updating to 2.17 fixed it
Thanks! ...
written 13 months ago by
fwuffy • 50
0
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1
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616
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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 13 months ago by
fwuffy • 50
2
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... 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
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1
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589
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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 15 months ago by
fwuffy • 50
2
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1
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589
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... 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 15 months ago by
fwuffy • 50
0
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2
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3.4k
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2
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Answer:
A: Number of Threads for BWA MEM
... Bump. You can not run bwa with 1000 threads on one host and expect it to be 1000x faster than single thread. There will be a theoretical optimum which is a function of memory available per thread and reference genome size. Has anyone actually done tests? ...
written 15 months ago by
fwuffy • 50
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For SnpSift annotate reporting extra alleles not present in the input VCF
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For Samtools mpileup quality scores all zero
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