User: fwuffy

gravatar for fwuffy
fwuffy90
Reputation:
90
Status:
Trusted
Location:
Michigan, USA
Website:
http://glyphdataservic...
Last seen:
1 month ago
Joined:
4 years, 8 months ago
Email:
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Software developer working in NGS analytics. 

Posts by fwuffy

<prev • 26 results • page 1 of 3 • next >
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BWA Mem -M flag (mark split hits) effect on structural variation calling
... 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 ...
structural-variations delly bwa written 4 weeks ago by fwuffy90 • updated 4 weeks ago by trausch1.4k
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Comment: C: Looking for a database containing the least-conserved, most highly polymorphic S
... Ok, thanks. I'll try that... ...
written 11 months ago by fwuffy90
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Looking for a database containing the least-conserved, most highly polymorphic SNPs (or regions) of the human genome (hg38)
... 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 ...
conservation human snp written 11 months ago by fwuffy90 • updated 11 months ago by colindaven1.9k
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Filtering VCF with vcf-tools using --maf=0.0001 filters out all homozygous calls ?!
... 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 ...
vcf vcf-tools filtering variants written 21 months ago by fwuffy90
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Can anyone tell me why BCFTools Call would call a homozygous variant at this position with 1/2 alt variant reads?
... 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 ...
vcf bcftools variants written 21 months ago by fwuffy90
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Comment: C: Picard MarkDuplicates fatal error
... Updating to 2.17 fixed it Thanks! ...
written 21 months ago by fwuffy90
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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 21 months ago by fwuffy90
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Picard MarkDuplicates fatal error
... 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 ...
picard markduplicates written 21 months ago by fwuffy90 • updated 21 months ago by h.mon29k
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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 22 months ago by fwuffy90
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VCF PL Values not making sense
... 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 ...
vcf written 22 months ago by fwuffy90

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

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