User: fwuffy

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fwuffy100
Reputation:
100
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Trusted
Location:
Michigan, USA
Website:
http://glyphdataservic...
Last seen:
3 months, 2 weeks ago
Joined:
5 years, 7 months ago
Email:
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Software developer working in NGS analytics. 

Posts by fwuffy

<prev • 29 results • page 1 of 3 • next >
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Comment: C: how to make a .tbi file of .gtf.gz?
... 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 fwuffy100
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Comment: C: Detailed process for building snpEff database for NCBI RefSeq genomes?
... 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 fwuffy100
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Detailed process for building snpEff database for NCBI RefSeq genomes?
... 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) ...
genome database snpeff written 4 months ago by fwuffy100
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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 12 months ago by fwuffy100 • updated 12 months ago by trausch1.5k
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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 22 months ago by fwuffy100
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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 22 months ago by fwuffy100 • updated 22 months ago by colindaven2.5k
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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 2.7 years ago by fwuffy100
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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 2.7 years ago by fwuffy100
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Comment: C: Picard MarkDuplicates fatal error
... Updating to 2.17 fixed it Thanks! ...
written 2.7 years ago by fwuffy100
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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 2.7 years ago by fwuffy100

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

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