User: fwuffy
fwuffy • 100
- Reputation:
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- Trusted
- Location:
- Michigan, USA
- Website:
- http://glyphdataservic...
- Last seen:
- 6 months, 3 weeks ago
- Joined:
- 5 years, 10 months ago
- Email:
- p******@gmail.com
Software developer working in NGS analytics.
Posts by fwuffy
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... 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 7 months ago by
fwuffy • 100
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... 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 7 months ago by
fwuffy • 100
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... 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 7 months ago by
fwuffy • 100
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... 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 ...
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... Ok, thanks. I'll try that... ...
written 2.2 years ago by
fwuffy • 100
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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 2.2 years ago by
fwuffy • 100
• updated
2.1 years ago by
colindaven • 2.6k
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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 3.0 years ago by
fwuffy • 100
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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 3.0 years ago by
fwuffy • 100
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Comment:
C: Picard MarkDuplicates fatal error
... Updating to 2.17 fixed it
Thanks! ...
written 3.0 years ago by
fwuffy • 100
0
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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 3.0 years ago by
fwuffy • 100
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8 months ago,
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For Samtools mpileup quality scores all zero
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13 months ago,
created a question with more than 1,000 views.
For SnpSift annotate reporting extra alleles not present in the input VCF
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created a question with more than 1,000 views.
For SnpSift annotate reporting extra alleles not present in the input VCF
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For BWA Mem -M flag (mark split hits) effect on structural variation calling
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For SnpSift annotate reporting extra alleles not present in the input VCF
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For SnpSift annotate reporting extra alleles not present in the input VCF
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