User: finswimmer

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finswimmer730
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730
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Germany
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2 hours ago
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11 months, 3 weeks ago
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Posts by finswimmer

<prev • 144 results • page 1 of 15 • next >
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Comment: C: Alignment & Variant Calling explanation SNP and SNV.
... Why do you think you have one file with "SNP" and one with "SNV"? "SNP" stands for "SIngle Nucleotide Polymorphism". And "SNV" for "Single Nucleotide Variation". The term SNP is more often used in talks. The problem is that "polymorphism" implice that the change in sequence is quite often and ha ...
written 6 hours ago by finswimmer730
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Comment: C: How to get SNP identifiers from VCF file?
... It looks like you are running out of memory. Try to limit the memory java can use by setting the `-Xmx` paramater. E.g. java -Xmx12G -jar SnpSift.jar annotate -id dbSnp.vcf your.vcf > annotated.vcf if you want to allow java to take 12GB. BTW: You should index the gzip'ed dbSnp file with ta ...
written 6 hours ago by finswimmer730
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Answer: A: How to get SNP identifiers from VCF file?
... Hello, what you are looking for is called "Annotating". There a couple of programs that can use other vcf/bed,/tab-delimited files which contains information that you want to see in your vcf. [bcftools][1] and [snpEff/SnpSift][2] are such programs . So first download the dbnSnp database ([hg19][3 ...
written 1 day ago by finswimmer730
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Answer: A: parsing vcf file
... First: > but it is not working isn't a good error description. Second: > Some people, when confronted with a problem, think “I know, I'll use > regular expressions.” Now they have two problems. :) I would do something like this: 1. split each vcf line by the column delimiter (tab ...
written 2 days ago by finswimmer730
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Comment: C: Sort VCF File by Position?
... Hello ATPoint, funny. This is exact the same reason why I use natural sorting. :) The data I've worked with (human) was always sorted this way and I got problems it a part in the analyse pipeline wasn't. fin swimmer ...
written 3 days ago by finswimmer730
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Comment: C: Sort VCF File by Position?
... sort -k1,1 -k2,2n This works well in your case, as you seem to have just on chromosome. For sorting a vcf file I prefer this: sort -k1,1V -k2,2n my.vcf This makes sure that your chromosomes are sorted correctly. WIthout the 'V' "2" comes behind "19" for example. fin simmer ...
written 3 days ago by finswimmer730
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Comment: C: Picard tools: error with CollectInsertSizeMetrics
... Are you sure that your bam file contains mapped paired end reads? What's the output of samtools flagstats? fin swimmer ...
written 3 days ago by finswimmer730
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Comment: C: Checking bam quality
... > So to check quality of both reads Please define what you mean by "quality". There are so many things one can look for and it maybe depends on the goal of your analysis. fin swimmer ...
written 17 days ago by finswimmer730
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Answer: C: bedtools genomecov -bg -split -ibam bamfile. error: the input file is not sorted
... Hello, I guess bedtools need the bam file sorted by coordinates and not by readnames as you do with `samtools sort -n`. And did you use sortedfile for redoing yohr test? fin swimmer ...
written 18 days ago by finswimmer730
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Comment: C: Help understanding CHROM and POS fields in VCF
... That was my thought either after sending my answer. In the linked example there is a header > ##reference=1000GenomesPilot-NCBI36 which is hg18. fin swimmer ...
written 4 weeks ago by finswimmer730

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