User: win

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win730
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730
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India
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1 month, 1 week ago
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5 years, 10 months ago
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Posts by win

<prev • 220 results • page 1 of 22 • next >
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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 5 weeks ago by win730
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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 6 weeks ago by win730 • updated 6 weeks ago by michael.ante2.4k
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Comment: C: VariantRecalibration step issue
... Thanks you very much. I will do as suggested. ...
written 8 weeks ago by win730
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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 9 weeks ago by win730
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Comment: C: Reference allele is too long message GATK
... No, thats the problem. ...
written 9 weeks ago by win730
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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 9 weeks ago by win730
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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 9 weeks ago by win730 • updated 9 weeks ago by WouterDeCoster27k
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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 9 weeks ago by win730
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Comment: A: QD Annotation error in GATK in VariantRecalibration step
... Any ideas as to why this is happening? ...
written 10 weeks ago by win730
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QD Annotation error in GATK in VariantRecalibration step
... hi all, i downloaded a BAM file from 1000 genomes to work on and converted it to FASTQ and aligned with bwa mem to hg38, this worked fine. later I wanted to run VariantRecalibration and use the following commands for SNP and they worked fine as well. java -Xmx8g -jar algorithms/gatk3/gatk.jar ...
ngs written 10 weeks ago by win730

Latest awards to win

Popular Question 7 weeks 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 genome coordinates for snps
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Great Question 12 months ago, created a question with more than 5,000 views. For Sample Exome Fastq Files
Student 12 months ago, asked a question with at least 3 up-votes. For Vcf Database Table Structure
Appreciated 12 months ago, created a post with more than 5 votes. For Samtools And Region List
Popular Question 16 months ago, created a question with more than 1,000 views. For Chromosomal Locus From Ucsc
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Great Question 16 months ago, created a question with more than 5,000 views. For Sample Exome Fastq Files

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