User: win
win • 730
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Posts by win
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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 5 weeks ago by
win • 730
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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 6 weeks ago by
win • 730
• updated
6 weeks ago by
michael.ante • 2.4k
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Comment:
C: VariantRecalibration step issue
... Thanks you very much. I will do as suggested. ...
written 8 weeks ago by
win • 730
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... same message, it seems like the --reference_window_stop is not working or has incorrect values. ...
written 9 weeks ago by
win • 730
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... No, thats the problem. ...
written 9 weeks ago by
win • 730
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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 9 weeks ago by
win • 730
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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 9 weeks ago by
win • 730
• updated
9 weeks ago by
WouterDeCoster ♦ 27k
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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 9 weeks ago by
win • 730
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... Any ideas as to why this is happening? ...
written 10 weeks ago by
win • 730
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... 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 ...
written 10 weeks ago by
win • 730
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