User: hellbio

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hellbio370
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Posts by hellbio

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Comment: C: SNP Count from telomeres in sliding window
... It still fails with the below error: INFO: trying MySQL /usr/bin/mysql for database hg38 Non-numeric start coordinate. See line 50 in -. (remember that chromosome names should not contain spaces.) However, if i have the chromosomes sizes in the below format is there a way without using fetch ...
written 4 months ago by hellbio370
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Comment: C: SNP Count from telomeres in sliding window
... It gives a syntax error at the semicolon after $2 : > awk: { printf("%s\t0\t%d\n%s\t%d\t%d\n", $1, bounds, $1, ($2 - bounds - 1), $2; } ^ syntax error ...
written 4 months ago by hellbio370
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Comment: C: SNP Count from telomeres in sliding window
... Here the issue is that we are working on model organism for which the telomeres are not defined and available in UCSC. Therefore, we work with an assumption of 20Mb or try 10Mb later to define the telomeres. I wonder how to do this with this assumption. ...
written 4 months ago by hellbio370
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Comment: C: SNP Count from telomeres in sliding window
... Thank you. Does the count table reports the count of SNPs from both ends of the telomeres in each chromosome? Ideally, it is only required to get the count of SNPs for example upto 20Mb from either ends of the chromosomes. The middle regions i.e. SNPs in the centromeres of the chromosomes are not re ...
written 4 months ago by hellbio370
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SNP Count from telomeres in sliding window
... Hi, I have a list of SNP genomic coordinates: a.txt chr1 12345 12345 chr1 32424 32424 chr4 23234 23234 .... .... chr22 332324 332324 I would like to find the count of SNPs i.e. from the start of the chromosomes in the genome with increasing ...
genome snp written 4 months ago by hellbio370 • updated 4 months ago by Alex Reynolds28k
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Comment: C: Mendelian Inheritance Rate (CNV)
... did you find a way to do this? i am in a similar situation. ...
written 9 months ago by hellbio370
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Human CNV VCF for Trios from whole-genomes
... Dear all, I am looking for CNVs in father-mother-child trios generated from whole-genome sequencing data. I have searched DGV and could find data from several projects including 1000genomes project. However, the data is in gvf format which does not have a sample specific genotypes in the file to i ...
wgs cnv trios written 9 months ago by hellbio370 • updated 9 months ago by trausch1.3k
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Comment: C: Genotype count in a VCF file
... I tried getSampleName() in the print statement. It won't do what i need, it is just printing one name for all the variants. Seems there is a little more complicated solution that needs some intuition. Could you help. out.println(ctx.getContig()+" "+ctx.getStart()+" "+JSON.stringify(m)+" ...
written 13 months ago by hellbio370
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Comment: C: Genotype count in a VCF file
... Hi Pierre, could we print the sample names also in separate columns corresponding to the counts? BTW, i could not find the jar in the git, is it moved to a different location or name? ...
written 13 months ago by hellbio370
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Comment: C: Genotype count in a VCF file
... could it be possible to print the sample names as well? ...
written 13 months ago by hellbio370

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