User: win

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win810
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810
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10 months ago
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6 years, 12 months ago
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Posts by win

<prev • 221 results • page 1 of 23 • next >
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Interpreting stats from gnomAD/ ExAC reference population
... Hello, I want to generate stats of various types of statistical information from reference population in gnomAD/ExAC reference population and wanted to know what might be the best way to accomplish this. Could not find any open-source tool/ script online and in some online code repos. Any help in ...
exac written 10 months ago by win810 • updated 10 months ago by manuel.belmadani870
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GATK joint genotyping
... Hi all, i am struggling a bit with preparing a cohort genome vcf file for joint genotyping using GATK. I tried with 30 BAMs from 1000 genomes, and generated a single sample VCF for each, then used GATK CombineVariants and produced a "master" gVCF file. This is not working during variant calling si ...
gatk ngs written 15 months ago by win810
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Genomic coordinates for transcripts
... Hi all, i have transcript IDs such as NM_001250.5, NM_000073.2 and many more. I wanted to know how could I get hg19 genomic coordinates for each one. I have tried this on UCSC genome browser and wanted to know if it can be automated. any pointers in this direction could be most helpful. thanks ...
ngs written 15 months ago by win810 • updated 15 months ago by michael.ante3.3k
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Comment: C: VariantRecalibration step issue
... Thanks you very much. I will do as suggested. ...
written 16 months ago by win810
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Comment: C: Reference allele is too long message GATK
... same message, it seems like the --reference_window_stop is not working or has incorrect values. ...
written 16 months ago by win810
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Comment: C: Reference allele is too long message GATK
... No, thats the problem. ...
written 16 months ago by win810
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Comment: C: Reference allele is too long message GATK
... OK, but there are other such messages as well, same message but differing length like some say 108, some are 150 etc. I have also set --reference_window_stop to 1000. ...
written 16 months ago by win810
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Reference allele is too long message GATK
... hi all, i generated a gVCF file using HaplotypeCaller. When i run ValidateVariants from GATK i get the message "Reference allele is too long (108) at position chr9:99423855; skipping that record. Set --reference_window_stop >= 108" Any ideas what is causing this? Command used to generate the g ...
vcf written 16 months ago by win810 • updated 16 months ago by WouterDeCoster39k
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VariantRecalibration step issue
... Hi all, i need some advice about VariantRecalibration as in if I am doing the right thing. Downloaded 30 bams from 1000 genomes and realigned them to HG38. Then using HaplotypeCaller generated a gVCF for each BAM. Then used CombineGVCFs and made a single VCF named cohort.g.vcf Took a sample BAM an ...
vcf written 16 months ago by win810
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Comment: A: QD Annotation error in GATK in VariantRecalibration step
... Any ideas as to why this is happening? ...
written 16 months ago by win810

Latest awards to win

Great Question 15 months ago, created a question with more than 5,000 views. For Promoter Or Enhancer Regions Bed Format
Popular Question 15 months ago, created a question with more than 1,000 views. For Generate GVF file from VCF file
Popular Question 15 months ago, created a question with more than 1,000 views. For BAM to individual chromosome fasta/fastq
Appreciated 15 months ago, created a post with more than 5 votes. For Samtools And Region List
Popular Question 15 months ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 15 months ago, created a question with more than 1,000 views. For Human GRCh38 and dbSNP VCF and GATK
Great Question 15 months ago, created a question with more than 5,000 views. For Create A Tbi File From Vcf
Popular Question 15 months ago, created a question with more than 1,000 views. For Reference genome in VCF format (gVCF)
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For Remove Vcf Header Lines
Popular Question 15 months ago, created a question with more than 1,000 views. For Length of sequences in FASTQ file
Great Question 15 months ago, created a question with more than 5,000 views. For Lift-over on a VCF
Popular Question 15 months ago, created a question with more than 1,000 views. For Get Reference file from BAM
Popular Question 15 months ago, created a question with more than 1,000 views. For Per chromosome gVCF
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Convert GVF to VCF
Popular Question 15 months ago, created a question with more than 1,000 views. For HG18 coordinates of rs#
Popular Question 15 months ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 22 months ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 22 months ago, created a question with more than 1,000 views. For genome coordinates for snps
Epic Question 22 months ago, created a question with more than 10,000 views. For Annotate A Vcf File
Popular Question 22 months ago, created a question with more than 1,000 views. For Human GRCh38 and dbSNP VCF and GATK
Popular Question 22 months ago, created a question with more than 1,000 views. For HG18 coordinates of rs#
Popular Question 22 months ago, created a question with more than 1,000 views. For Sample Exome Fastq Files
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Sample Exome Fastq Files
Great Question 2.2 years ago, created a question with more than 5,000 views. For Sample Exome Fastq Files
Appreciated 2.2 years ago, created a post with more than 5 votes. For Samtools And Region List

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