User: BAGeno

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BAGeno170
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Posts by BAGeno

<prev • 88 results • page 1 of 9 • next >
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Answer: A: Bcftools filter error
... I am using bcftools 1.9. Do I need to install latest version? ...
written 4 days ago by BAGeno170
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Comment: C: Bcftools filter error
... Yes it is multi-sample vcf and GQ field is in FORMAT column. Here are lines of -e option. chr1 3787134 rs41307854 A G 1543.55 PASS AC=5;AF=0.167;AN=30;BaseQRankSum=-0.367;DB;DP=342;ExcessHet=4.7216;FS=0.688;InbreedingCoeff=-0.2;MLEAC=5;MLEAF=0.167;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD ...
written 4 days ago by BAGeno170
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Bcftools filter error
... Hi, I am using bcftools filter. I run bcftools filter command in two different ways. It gave me different results. Command #1 bcftools filter --e "GQ<20" miss.GT.vcf.gz>test1.vcf This gave me `49336` variants. while when I run command 2 bcftools filter -i "GQ>20" miss.GT.vc ...
filter bcftools written 4 days ago by BAGeno170
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Plot-vcfstats not installed
... Hi, I have installed bcftools 1.9. I am analzying output produced by bcftools stats by running following command plot-vcfstats -p outdir test.vchk It gives me error of `The program 'plot-vcfstats' is currently not installed`. Can you please tell me how to solve this problem? ...
bcftools plot-vcfstats written 5 days ago by BAGeno170
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Problem with allele frequency calculation in vcf
... Hi, I am encountering problem in vcf related to allele frequency. Here is my sample file. chr1 113834946 rs2476601 A G,T 938986 PASS AC=21,1;AF=0.983315,0.000538213;AN=22;BaseQRankSum=1.13;ClippingRankSum=0.217;DP=33382;ExcessHet=4.0054;FS=0;InbreedingCoeff=-0.0158;MLEAC=1897,1;MLEAF=0.984,0.0 ...
vcf allele frequency written 10 months ago by BAGeno170
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Contra control file
... Hi, I am want to find copy number variations in my exome sequencing data. For this purpose i would like to use `contra`. I do not have control bam so can I use bam file of 1000 genome as my control? ...
contra cnv written 12 months ago by BAGeno170 • updated 11 months ago by halina0
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Comment: C: Tranche Plot after VSQR
... @Nicolas Is ![this ][1] OK? Should I make `--truth-sensitivity-filter-level` 99.9 in `ApplyVQSR`. [1]: https://drive.google.com/file/d/1z18aycmkL3PE3yM3Pe_sFeDC6t3nTTR_/view?usp=sharing ...
written 12 months ago by BAGeno170
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Comment: C: Tranche Plot after VSQR
... @Nicolas I have made GVCF with interval file having size of about 400MB. Previously their size of 3 GB. Is this right or I am making mistake somewhere? ...
written 12 months ago by BAGeno170
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Comment: C: Tranche Plot after VSQR
... Is it necessary to include 1000 genomes bam? As I have machine of low RAM ...
written 13 months ago by BAGeno170
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Comment: C: Tranche Plot after VSQR
... I have used GATK 4.0.8. I run `HaplotypeCaller`, `CombineGVCFs`, and `GenotypeGVCFs`. I did not use interval file. So what should I do for this? ...
written 13 months ago by BAGeno170

Latest awards to BAGeno

Popular Question 10 months ago, created a question with more than 1,000 views. For Vcftools gives error when extracting snps
Popular Question 10 months ago, created a question with more than 1,000 views. For Whole Exome CNV tools
Popular Question 10 months ago, created a question with more than 1,000 views. For GC content and average fold coverage of contigs
Popular Question 10 months ago, created a question with more than 1,000 views. For Bcftools merge taking too much time and producing large file
Popular Question 10 months ago, created a question with more than 1,000 views. For Difference between read and contig based taxonomic classification
Popular Question 10 months ago, created a question with more than 1,000 views. For EBI SRA FTP is not working
Popular Question 10 months ago, created a question with more than 1,000 views. For GC content and average fold coverage of contigs
Popular Question 10 months ago, created a question with more than 1,000 views. For Difference between read and contig based taxonomic classification
Popular Question 10 months ago, created a question with more than 1,000 views. For Vcftools gives error when extracting snps
Supporter 13 months ago, voted at least 25 times.
Popular Question 16 months ago, created a question with more than 1,000 views. For EBI SRA FTP is not working
Popular Question 16 months ago, created a question with more than 1,000 views. For Difference between read and contig based taxonomic classification
Popular Question 16 months ago, created a question with more than 1,000 views. For How to run bcftools roh with multiple samples vcf
Popular Question 20 months ago, created a question with more than 1,000 views. For EBI SRA FTP is not working
Popular Question 22 months ago, created a question with more than 1,000 views. For VEP and Annovar Annotation
Popular Question 23 months ago, created a question with more than 1,000 views. For Grep Position List

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