User: Satyajeet Khare

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Satyajeet Khare1.4k
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Posts by Satyajeet Khare

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Comment: C: DE novo call from trio
... The link did not open, but assuming that you have a vcf file from the same source and corresponding to the same genome version you used for alignment, it should work. But I would still recommend using GATK bundle since you may need some files in future which are exclusively present in the GATK bundl ...
written 23 days ago by Satyajeet Khare1.4k
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Comment: C: DE novo call from trio
... Yes, you need to perform the alignment again. I think it will affect the outcome because the coordinates of the vcf file won't match the alignment files in current scenario. ...
written 25 days ago by Satyajeet Khare1.4k
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Comment: C: DE novo call from trio
... Oh, its select biallelic. Anyway, as I mentioned, I never had to do this step. Regarding the last point (and this may get rid of this biallelic issue), you need to use b37 package for all files. Assuming you downloaded the vcf file `1000G_phase1.snps.high_confidence.b37.vcf.gz` from [this link][1] ...
written 25 days ago by Satyajeet Khare1.4k
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Comment: C: DE novo call from trio
... No, gvcf wont change the results. Just that adding samples later will be easier. I am not sure why "convert to biallelic" step is necessary. I also worked only on SNPs but did not run this command. Everything else looks fine. What were the hard filtration parameters? Important: You may want to use ...
written 29 days ago by Satyajeet Khare1.4k
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Comment: C: DE novo call from trio
... Its possible. But I think following change would help. 1. After BQSR, create g.vcf files for each sample using `HaplotypeCaller` `-ERC GVCF` option. 2. Create a combined genotype using `GenotypeGVCFs` 3. Separate SNPs and Indels using `SelectVariants` and perform hard filtration 4. Comb ...
written 29 days ago by Satyajeet Khare1.4k
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Removing the tagged variants after variant filtration step
... I am analysing 18 exome sequencing samples for identification of germline variants. I separated the SNPs and Indels from the genotype.vcf file using SelectVariants and performed hard filtration as recommended [here][1]. Now I have merged the SNPs and Indels into one file using `CombineVariants` and ...
gatk snp written 10 weeks ago by Satyajeet Khare1.4k
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Answer: A: Error in match.arg in boxplot - oligo package
... Try boxplot(rawData, "all", las=3) ...
written 4 months ago by Satyajeet Khare1.4k
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Comment: C: RNA-seq Data Excel Formatting
... You can use any simple text editor to get your genes of interest in this format `goi_1|goi_2|goi_3` etc. Next, try `grep` like this grep -E "goi_1|goi_2|goi_3" expression_matrix.txt You can also save the output as grep -E "goi_1|goi_2|goi_3" expression_matrix.txt > output.txt ...
written 8 months ago by Satyajeet Khare1.4k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... The issue is resolved. I made two changes. I don't know which one worked. 1. I had skipped the local realignment step earlier. That is, I had used the `Picard` output directly for BQSR. I corrected the pipeline by incorporating that step. 2. I used genome.fasta and all .vcf files from gatk resourc ...
written 9 months ago by Satyajeet Khare1.4k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... Thanks, I will try running without `-an QD` parameter, but here are a couple of other peculiar observations. 1. I do see QD annotations in my VCF file, even without running the `VariantAnnotator` also. 2. If I try and validate the resource VCF files from [gatk resource bundle][1] (1000G and hapmap) ...
written 9 months ago by Satyajeet Khare1.4k

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Popular Question 15 days ago, created a question with more than 1,000 views. For Differential expression analysis with RNA-Seq samples that vary in depth
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Popular Question 7 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
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