User: finswimmer77

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finswimmer77130
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Posts by finswimmer77

<prev • 22 results • page 1 of 3 • next >
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Comment: C: When I install samtools, the linux cannot find -lcurses and cannot find -lz. How
... And beside this question, are you trying to install samtools via the package manager of your linux version or by compiling it? fin swimmer ...
written 1 day ago by finswimmer77130
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Comment: C: GATK - gene panel VCF - too many variants - how to filter out
... Is this just a typo here? Your output file from MarkDuplicates is `1234_dedup.bam` but in the next steps you use `1234_remdup.bam` as the input file name. fin swimmer ...
written 17 days ago by finswimmer77130
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Comment: C: GATK - gene panel VCF - too many variants - how to filter out
... Hello, 40 000 variants in 112 genes. That's much to much. Can you post the commands you use for the alignment and variant calling? And also the first few entrys of your vcf file are interessting. fin swimmer ...
written 20 days ago by finswimmer77130
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Comment: C: how to get the coverage for the entire interval
... Hello, what was the command you used? And how do you define "coverage"? Total bases sequenced? Average read counts per position? ..? For `bedtools coverage` for example there is option `-d`, which reportes the depth at each position even if it's zero. fin swimmmer ...
written 26 days ago by finswimmer77130
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Comment: C: Is it necessery to perform GATK-BQSR before performing variant calling using fre
... Hello, just follow the link in my post and you will find it. A copy and paste from the website: > FreeBayes incorporates a number of features in order to reduce the > complexity of variant detection for researchers and developers: > > Indel realignment is accomplished internally using ...
written 26 days ago by finswimmer77130
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Comment: C: How to convert .vcf files into .csv?
... Hi, how should your mysql datatable look like? As in the vcf file the columns are tab-seperated you allready have a format you can import via phpmyadmin. But if you want to spilt the several fields in the INFO column, more work is needed. fin swimmer ...
written 4 weeks ago by finswimmer77130
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Comment: C: pythonic way to get gene_id, gene_symbol from given list of gene, transcript co-
... Hello, you could use ensembl's [REST-Api][1] for this, e.g. the Overlap endpoint. fin swimmer [1]: http://rest.ensembl.org ...
written 5 weeks ago by finswimmer77130
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Comment: C: Faster way to get coverage per base
... I didn't try sambamba until now. But I recognize that picards CollectHsMetrics have an PER_BASE_COVERAGE option. As I'm running CollectHsMetrics in any case I could use this option. fin swimmer ...
written 7 weeks ago by finswimmer77130
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Comment: C: Understanding Picards HsMetrics
... Hello Pierre, that makes it a little bit clearer. So ON_TARGET means here only those bases of read which are realy mapped to a target position, and ON_BAIT counts also those bases that are not strictly mapped to a reference position but "somewhere between" (insertions) or are clipped? Is the ratio ...
written 7 weeks ago by finswimmer77130
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Understanding Picards HsMetrics
... Hello, I have some problems understanding the output of picards CollectHsMetrics. Because I don't have a bait file i uses my bed file with the target regions to produce the interval list. java -jar picard.jar BedToIntervalList I=target.bed SD=genome.dict O=target.interval_list This target int ...
picardtools bam sam written 7 weeks ago by finswimmer77130 • updated 7 weeks ago by Pierre Lindenbaum94k

Latest awards to finswimmer77

Commentator 7 weeks ago, created a comment with at least 3 up-votes. For A: sam file error
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file

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