User: oars

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oars110
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Posts by oars

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Variant Calls: Freebayes vs GATK
... Many thanks for your reply! Here are the two call scripts, maybe this would be insightful: $ GATK HaplotypeCaller -I SRR1611183.dedup.bam -O SRR1611183.gatk.vcf -R genome.fa -L chr17.cds.bed and for freebayes... $ freebayes -f genome.fa -m 20 -q 10 -t chr17.cds.bed SRR1611183.dedup.bam & ...
written 7 weeks ago by oars110
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Comment: C: Simple count of dbSNP (rs...) from .vcf file
... I came up with a solution: awk '$3=="." {print $0}' SRR1611183.gatk.dbsnp.vcf > ID_nulls.vcf ...
written 8 weeks ago by oars110
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Comment: C: Variant Calls: Freebayes vs GATK
... When examining the tail end of data found in the INFO column, you'll notice a difference between GATK and Freebayes: GATK GT:AD:DP:GQ:PL 1/1:0,65:65:99:2535,196,0 Freebayes GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2261:-5,-5,0 Can anyone decipher this information? ...
written 8 weeks ago by oars110
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Comment: C: Simple count of dbSNP (rs...) from .vcf file
... Thanks - I actually do have rs numbers in the ID field so I'm not sure whats going on. For example, I pasted the data into excel and found out of 1761 variants (POS) and 1467 (83%) had dbSNPs (rs...) identified. I just can't figure out a simple way to cut and count the rs#'s in the file as is. I ...
written 8 weeks ago by oars110
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Comment: C: Variant Calls: Freebayes vs GATK
... Thanks! vcftools has a feature called --diff vcftools --vcf SRR1611183.gatk.vcf --diff SRR1611183.freebayes.vcf --diff-site --out gatk_freebayes.diff It creates a neat outfile with the following contents; CHROM POS1 POS2 IN_File REF1 REF2 ALT1 ALT2 chr17 5036281 5036281 B G G C C ...
written 8 weeks ago by oars110
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Variant Calls: Freebayes vs GATK
... I'm calling variants using three input/reference files (dedup.bam; genome.fa; and chr17.cds.bed) and creating two vcf files, (1) for gatk.vcf and (2) freebayes.vcf. GATK returned more variants (POS) and more dbSNPs. Scanning the files you quickly notice the different quality scores between the two ...
.vcf gatk freebayes written 8 weeks ago by oars110 • updated 8 weeks ago by vdauwera750
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Comment: C: Identifying Heterozygous Variants in VCF file using vcftools or bcftools
... Kevin - this is brilliant! Works perfectly, all I needed to do was sum up the 1's in excel. ...
written 8 weeks ago by oars110
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Comment: C: Simple count of dbSNP (rs...) from .vcf file
... A bunch of header information, then a series of "." . . . ...
written 8 weeks ago by oars110
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Comment: C: Simple count of dbSNP (rs...) from .vcf file
... ##fileformat=VCFv4.2 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ...
written 8 weeks ago by oars110
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Comment: C: Simple count of dbSNP (rs...) from .vcf file
... thanks for the reply. This returns 0. I've also tried to count the nulls with the following linux command but also returned 0: cut -f3 SRR1611183.gatk.vcf | grep -v "." | wc -l ...
written 8 weeks ago by oars110

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