User: Kevin

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Kevin590
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Posts by Kevin

<prev • 41 results • page 1 of 5 • next >
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Answer: A: Creating A New File by Combining Two Separate Files
... might need to loop twice, once to create a new column that's conditional on the 2nd column then using https://stackoverflow.com/questions/37697195/how-to-merge-two-data-frames-based-on-particular-column-in-pandas-python to create your final output file? perhaps inefficient but how many rows do you ...
written 4 months ago by Kevin590
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Comment: C: randomly subsampling a bam file three times
... in case it's not apparent , PROBABILITY=Double P=Double The probability of keeping any individual read, between 0 and 1. Default value: 1.0. This option can be set to 'null' to clear the default value. use 0.25 for ~ 25% of the reads. ...
written 11 months ago by Kevin590
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Answer: A: Where Can I Find Data Setnormal\Tumor Of Cancer?
... Other possible sources which have other kinds of datasets European Genome-phenome Archive https://www.ebi.ac.uk/ega/datasets EGAD00001000082 20 Matched Pair Breast Cancer Genomes Illumina HiSeq 2000, Illumina Genome Analyzer II 42 bam https://www.ebi.ac.uk/ega/datasets/EGAD00001000082 https://dis ...
written 20 months ago by Kevin590
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Answer: A: 10Kb Reads From Illumina Hiseq
... The first set of public data is out already. they have 3000 8500bp reads (single end) http://kevin-gattaca.blogspot.sg/2013/07/what-would-you-do-with-3k-of-8500-bp.html ...
written 5.0 years ago by Kevin590
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Convert Illumina Human Hapmap 550 K Chip Manifest File From B36 To B37
... Hi I have old data that was genotyped on convert Illumina Human Hapmap 550 k chip the old manifest file is in b36. What's the best way to migrate this info to b37? I know one approach was to use bwa to align the probes and annotating the sam file. But I googled and can't find a tool that does t ...
illumina convert written 5.8 years ago by Kevin590 • updated 5.8 years ago by Istvan Albert ♦♦ 77k
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Answer: A: Best Practices / Faster Samtools Mpileup, Any Tips?
... Ok just learnt about the new calling by region option in mpileup. Calling SNPs/INDELs in small regions (see http://samtools.sourceforge.net/mpileup.shtml ) vcfutils.pl splitchr -l 500000 ref.fa.fai | xargs -i \ echo samtools mpileup -C50 -m3 -F0.0002 -DSuf ref.fa -r {} -b bam.list \| bcftoo ...
written 5.9 years ago by Kevin590
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Comment: C: Split Bam Files By Region For Parallel Variant Calling
... Not a direct answer but GATK 2 has support for reduced bams now so they might reduce your bam sizes for multi sample calling. but of course if your issue is getting more chunks to parallelise then I think the samtools -L bedfile seems like a good idea ...
written 6.0 years ago by Kevin590
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Comment: C: Putting Run/Lane Info Back Into Readgroup For Gatk Pipeline
... As I understand, the RG field info can be found in the read name? e.g. format of the template name (header in the bam file), is it in the format of sequencer:lane:tile:coord-x:coord-y? Machine>_Run number> : Lane> : Tile> : X coordinate of cluster> : Y coordinate of cluster> ...
written 6.0 years ago by Kevin590
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Putting Run/Lane Info Back Into Readgroup For Gatk Pipeline
... I am looking at the read name from the archival bam from the sequencing provider. It provides machine/ run / lane info but readgroup info isn't written in it. What are my options if I want to extract the fastq from the bam to align with BWA to annotate the RG info so that it is used in downstream ...
gatk bam written 6.0 years ago by Kevin590 • updated 6.0 years ago by Sean Davis24k
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Comment: C: Bwa Aln -Q 15 When To Use It? What Does It Do?
... Thanks for the helpful links! I must have been using wrong keywords to search ...
written 6.0 years ago by Kevin590

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Prophet 11 months ago, created a post with more than 20 followers. For Where Can I Download Vcf Files For Publicly Available Data?
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Great Question 20 months ago, created a question with more than 5,000 views. For Fastest Way To Rename Sample Name In 37 Gb Gzipped Vcf File Or Binary Ped File
Great Question 20 months ago, created a question with more than 5,000 views. For Best Practices / Faster Samtools Mpileup, Any Tips?
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Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Per
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Bwa Aln -Q 15 When To Use It? What Does It Do?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For How To Extract Snps From A Desired List Of Gene Names
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Convert Illumina Human Hapmap 550 K Chip Manifest File From B36 To B37
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Snps In Promoter Regions In Exome Sequencing?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Where Can I Download Vcf Files For Publicly Available Data?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Fastest Way To Rename Sample Name In 37 Gb Gzipped Vcf File Or Binary Ped File
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Vcftools Can'T Create Ped Map File Due To Ulimit Of Allowed Open Files.
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Bigger Sample Sizes For Wgs Exome. Is Nosql The Way To Go? Or Bio Hdf
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Best Practices / Faster Samtools Mpileup, Any Tips?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Is There A Tool To Combine Samtools / Sam File Bitwise Flags?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Putting Run/Lane Info Back Into Readgroup For Gatk Pipeline
Popular Question 5.0 years ago, created a question with more than 1,000 views. For How To Create Genome-Wide Estimation Of Ibd Sharing Using Plink From Tped Files?
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