User: pinnintilikithreddy

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Posts by pinnintilikithreddy

<prev • 9 results • page 1 of 1 • next >
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Comment: C: snpEFF not able to download GRCH38 ?
... Sorry, its working with 38.86 ...
written 9 months ago by pinnintilikithreddy0
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Comment: C: snpEFF not able to download GRCH38 ?
... I tried with 38.86 showing same error ? ...
written 9 months ago by pinnintilikithreddy0
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Comment: C: BAN - Best alignment normalisation error
... Hi, Is it normalization should be performed for a raw vcf file isn't ? Thanks! ...
written 10 months ago by pinnintilikithreddy0
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Comment: C: How to extract specific chromosome from vcf file
... Hi I want to separate only chr21 from vcf how to do it. I tried above commands its not generating. can any one help me. Thanks for your suggestions. ...
written 10 months ago by pinnintilikithreddy0
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Comment: C: SNPSVM - not able to find VCF file
... HI Sorry, for late response, I given the path still it is not generating the output file. ...
written 10 months ago by pinnintilikithreddy0
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Comment: C: SNPSVM - not able to find VCF file
... Hi, again same error **Command:** [guest@ibscmachine SNPSVM-master]$ java -jar snpsvm.jar predict -R /data/guest/Softwares/novocraft/hg38.fa -B /data/guest/SNPSVM/SRR098401mem_pesort.bam -M /data/guest/Softwares/SNPSVM-master/models/default.model -V /data/guest/SNPSVM/SRR098401SNPSVM_mem1.raw.vcf Lo ...
written 11 months ago by pinnintilikithreddy0
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SNPSVM - not able to find VCF file
... I generated a sorted bamfile what to call variants. I provided a list of files. hg38.fa, hg38.fa.fi (indexfile) ,SRR098401_PE_bwtsort.bam,SRR098401mem_pesortbam (indexfile), Aligner - Bowtie2 Variant - SNPSVM I want to known whether it is running correctly ? Prompt Seems to be like this. I'm not ab ...
sequence written 11 months ago by pinnintilikithreddy0 • updated 11 months ago by pfs250
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Bowtie2 aligner not generating .sam file.
... Hi, I used bowtie2 V2.3.3.1 1st Step- bowtie2-build -f /media/likith/REDDY/CANCERGENOMICS/NewFolder/hg38.fa hg38 Generated a list of files- hg38.1.bt2, hg38.2.bt2,hg38.3.bt2,hg38.4.bt2,hg38.fa, hg38.rev.1.bt2, hg38.rev.2.bt2 2nd Step- bowtie2 -x hg38 -1 /media/likith/REDDY/CANCERGENOMICS/NewFolder ...
alignment written 11 months ago by pinnintilikithreddy0 • updated 11 months ago by Seigfried60
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(Closed) GATK HaplotypeCaller error ?
... Hi, I tried to generated a .VCF file using GATK HaplotypeCaller. I provided all the input requirements hg38.fa, hg38.dict, hg38.fa.fi and Bam file. Java 1.8 and picard I'm getting this error, kindly reply. Command : java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/likith/Downloads/Gen ...
genome alignment written 11 months ago by pinnintilikithreddy0 • updated 11 months ago by WouterDeCoster34k

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