User: Caddymob

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Caddymob950
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950
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Location:
United States
Website:
http://corneveaux.com
Last seen:
4 years, 11 months ago
Joined:
7 years, 8 months ago
Email:
j****@corneveaux.com

Molecular biologist turn bioinformatician. Hacking away at the Noah's Ark of genomes!

Posts by Caddymob

<prev • 57 results • page 1 of 6 • next >
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Answer: A: Plink bed files not recognized by samtools or bedtools
... A plink bed file is a binary PED, not a text BED - totally different... See the UCSC page for the format: http://genome.ucsc.edu/FAQ/FAQformat.html ...
written 5.0 years ago by Caddymob950
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Answer: A: Convert SAM to BAM
... Try `samtools import`. ~> samtools import Usage: bamtk import <in.ref_list> <in.sam> <out.bam>   ...
written 5.1 years ago by Caddymob950
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Answer: A: How to safely split a fasta file with concatenated multiple fasta sequences
... Check out bioawk from Heng Li: https://github.com/lh3/bioawk - and the great tutorial from Vince Buffalo  https://github.com/vsbuffalo/bioawk-tutorial ...
written 5.3 years ago by Caddymob950
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Answer: A: Customize IGV coverage track in R
... GATK DepthOfCoverage http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html or Bedtools genomecov http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html  are probably your best bet  ...
written 5.3 years ago by Caddymob950
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Answer: A: Piping Input Into Picard Sortsam
... Yes, picard (and most java apps should) take pipes. I do query sorts to FASTQs like this as one example: java -Xmx30g -jar ${PICARD}/SortSam.jar \ I=$IN_BAM \ TMP_DIR=${TMP} \ MAX_RECORDS_IN_RAM=7000000 \ VALIDATION_STRINGENCY=LENIENT \ COMPRESSION_LEVEL=0 \ O=/dev/stdout \ SORT_ORDER=queryname | \ ...
written 5.9 years ago by Caddymob950
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Comment: C: Chrx Genotype Counts In Esp6500 Exomes
... Oh, well, I'm supposing its male/female. For something on a non X-chr, you get like EA_GTC=6,344,2816 -- three numbers of genotypes. So why 5 on X Chr SNPs? ...
written 6.5 years ago by Caddymob950
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Chrx Genotype Counts In Esp6500 Exomes
... Does anyone know the format of how the NHLBI reports the genotypes for chromosome X varriants? If we look at the example rs6525447 we get strange stuff... In the VCF format we see EA_GTC=31,406,170,1991,1700 Heres the whole entry with the VCF header for completeness: ##fileformat=VCFv4.0 ##INFO=& ...
vcf written 6.5 years ago by Caddymob950
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Answer: A: Plink/Seq Denovo Option
... I figured it out. Here's the steps... Key is to load in your VCF first then annotate the pedigree. pseq proj1 load-vcf --vcf MY.vcf pseq proj1 load-pedigree --file msa.fam pseq proj1 denovo > MYdenovo.megaLists.txt Easy! ...
written 6.5 years ago by Caddymob950
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Plink/Seq Denovo Option
... Was looking at the PLINK/SEQ package today for pulling out denovo variants and munging around in my VCFs. The manual really has nothing on the denovo functuib, and testing the command, I get this... Any ideas what all these mean? pseq MyTest.vcf denovo --param pseq error : expect --param DP(kid) D ...
vcf plink denovo written 6.5 years ago by Caddymob950
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Comment: C: What To Do With 5-10K Usd For Computing Equipment
... with academic/non-profit pricing through Dell it was around 10K I recall.... ...
written 6.9 years ago by Caddymob950

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