User: Satyajeet Khare

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Satyajeet Khare1.5k
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Posts by Satyajeet Khare

<prev • 290 results • page 2 of 29 • next >
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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 months ago by Satyajeet Khare1.5k
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Answer: A: Error in match.arg in boxplot - oligo package
... Try boxplot(rawData, "all", las=3) ...
written 12 months ago by Satyajeet Khare1.5k
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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 16 months ago by Satyajeet Khare1.5k
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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 17 months ago by Satyajeet Khare1.5k
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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 17 months ago by Satyajeet Khare1.5k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... Mine is a small dataset (4 samples). Is that the problem? Should I just shift to hard filtration such as this? QD<2.0||MQ<40.0||FS>60.0||MQRankSum<-12.5||ReadPosRankSum<-8.0 ...
written 17 months ago by Satyajeet Khare1.5k • updated 16 months ago by RamRS27k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... Thanks @toralmanvar. I tested the input vcf file like this java -jar GenomeAnalysisTK.jar -T ValidateVariants --reference_window_stop >= 300 -R Homo_sapiens.GRCh38.dna.primary_assembly.fa --variant:VCF gatk_out/output_annotated.vcf The command finished the run without any errors. But the ou ...
written 17 months ago by Satyajeet Khare1.5k • updated 16 months ago by RamRS27k
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ERROR MESSAGE: QD annotation at VariantRecalibrator
... I am performing trio analysis with Exome sequencing data. I am using GATK 3.8. I am at VariantRecalibrator stage. Following is my command... java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -input /gatk_out/output.vcf --resource:hapmap,known= ...
gatk variantrecalibrator snp written 17 months ago by Satyajeet Khare1.5k • updated 16 months ago by Biostar ♦♦ 20
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Comment: C: Reference allele is too long message GATK
... This worked fine for me. java -jar GenomeAnalysisTK.jar -T ValidateVariants --reference_window_stop >= 300 -R Genome.fa --variant:VCF All.vcf.gz ...
written 17 months ago by Satyajeet Khare1.5k
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Comment: C: Convert colorspace fastq to basespace fastq
... Assuming that the data you need is not available on any other platform, you may want to use colorspace reads directly for the analysis. No need to convert the reads. You can use Tophat with bowtie1 option. Use bowtie version 0.12.7 or lower. ...
written 19 months ago by Satyajeet Khare1.5k

Latest awards to Satyajeet Khare

Great Question 3 months ago, created a question with more than 5,000 views. For fastq dump error
Popular Question 6 months ago, created a question with more than 1,000 views. For SpliceR genome session error
Scholar 6 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Popular Question 8 months ago, created a question with more than 1,000 views. For Differential expression analysis with RNA-Seq samples that vary in depth
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Popular Question 16 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 16 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 19 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Too low mapping percentage using HISAT2 on human reference genome.
Voter 2.2 years ago, voted more than 100 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Differentiall analysis of chip-deq data
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 2.4 years ago, created an answer that has been accepted. For A: error in tophat2
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 2.4 years ago, created an answer that has been accepted. For A: error in tophat2
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 2.6 years ago, created an answer that has been accepted. For A: error in tophat2
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Scholar 2.7 years ago, created an answer that has been accepted. For A: error in tophat2
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Scholar 2.7 years ago, created an answer that has been accepted. For A: error in tophat2
Scholar 2.7 years ago, created an answer that has been accepted. For A: error in tophat2

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