User: win

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win790
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790
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India
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1 month, 3 weeks ago
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6 years, 3 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 8 weeks ago by win790 • updated 8 weeks ago by manuel.belmadani60
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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 7 months ago by win790
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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 7 months ago by win790 • updated 7 months ago by michael.ante2.6k
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Comment: C: VariantRecalibration step issue
... Thanks you very much. I will do as suggested. ...
written 7 months ago by win790
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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 7 months ago by win790
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Comment: C: Reference allele is too long message GATK
... No, thats the problem. ...
written 7 months ago by win790
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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 7 months ago by win790
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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 7 months ago by win790 • updated 7 months ago by WouterDeCoster32k
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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 7 months ago by win790
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Comment: A: QD Annotation error in GATK in VariantRecalibration step
... Any ideas as to why this is happening? ...
written 8 months ago by win790

Latest awards to win

Great Question 7 months ago, created a question with more than 5,000 views. For Promoter Or Enhancer Regions Bed Format
Popular Question 7 months ago, created a question with more than 1,000 views. For Generate GVF file from VCF file
Popular Question 7 months ago, created a question with more than 1,000 views. For BAM to individual chromosome fasta/fastq
Appreciated 7 months ago, created a post with more than 5 votes. For Samtools And Region List
Popular Question 7 months ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 7 months ago, created a question with more than 1,000 views. For Human GRCh38 and dbSNP VCF and GATK
Great Question 7 months ago, created a question with more than 5,000 views. For Create A Tbi File From Vcf
Popular Question 7 months ago, created a question with more than 1,000 views. For Reference genome in VCF format (gVCF)
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Remove Vcf Header Lines
Popular Question 7 months ago, created a question with more than 1,000 views. For Length of sequences in FASTQ file
Great Question 7 months ago, created a question with more than 5,000 views. For Lift-over on a VCF
Popular Question 7 months ago, created a question with more than 1,000 views. For Get Reference file from BAM
Popular Question 7 months ago, created a question with more than 1,000 views. For Per chromosome gVCF
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Convert GVF to VCF
Popular Question 7 months ago, created a question with more than 1,000 views. For HG18 coordinates of rs#
Popular Question 7 months ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 13 months ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 13 months ago, created a question with more than 1,000 views. For genome coordinates for snps
Epic Question 13 months ago, created a question with more than 10,000 views. For Annotate A Vcf File
Popular Question 13 months ago, created a question with more than 1,000 views. For Human GRCh38 and dbSNP VCF and GATK
Popular Question 13 months ago, created a question with more than 1,000 views. For HG18 coordinates of rs#
Popular Question 13 months ago, created a question with more than 1,000 views. For Sample Exome Fastq Files
Popular Question 18 months ago, created a question with more than 1,000 views. For Sample Exome Fastq Files
Great Question 18 months ago, created a question with more than 5,000 views. For Sample Exome Fastq Files
Appreciated 18 months ago, created a post with more than 5 votes. For Samtools And Region List

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