User: win
win • 860
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Posts by win
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... 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 ...
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... 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 ...
written 2.7 years ago by
win • 860
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... 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 ...
written 2.7 years ago by
win • 860
• updated
2.7 years ago by
michael.ante • 3.6k
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Comment:
C: VariantRecalibration step issue
... Thanks you very much. I will do as suggested. ...
written 2.8 years ago by
win • 860
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... same message, it seems like the --reference_window_stop is not working or has incorrect values. ...
written 2.8 years ago by
win • 860
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... No, thats the problem. ...
written 2.8 years ago by
win • 860
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... 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 2.8 years ago by
win • 860
1
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1
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... 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 ...
written 2.8 years ago by
win • 860
• updated
2.8 years ago by
WouterDeCoster ♦ 44k
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... 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 ...
written 2.8 years ago by
win • 860
0
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2.5k
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... Any ideas as to why this is happening? ...
written 2.8 years ago by
win • 860
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