User: Edoardo Giacopuzzi

Reputation:
60
Status:
New User
Location:
Brescia, Italy
Last seen:
7 years, 1 month ago
Joined:
7 years, 9 months ago
Email:
g*********@gmail.com

Posts by Edoardo Giacopuzzi

<prev • 3 results • page 1 of 1 • next >
18
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3
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8.5k
views
10 follow
3
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Karyotypically Ordered Hg19
... Hi, I have a .bam file generated using the hg19 release of human genome downloaded from UCSC database. Now I'm trying to indentificate genomic variants using GATK UnifiedGenotyper but it returns an error cause my bam file is Lexicographically sorted. I've tried to use Picard ReorderSam function bu ...
gatk reference hg written 7.8 years ago by Edoardo Giacopuzzi60 • updated 4.5 years ago by Biostar ♦♦ 20
0
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1
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3.8k
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1
answers
Comment: C: Error With Gatk Unified Genotyper And Picard Bam File
... Thanks! It seems that adding VALIDATION_STRINGENCY option as you indicated solved the problem with Picard and now also GATK works fine. ...
written 7.8 years ago by Edoardo Giacopuzzi60
7
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1
answer
3.8k
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1
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Error With Gatk Unified Genotyper And Picard Bam File
... Hi, I'm trying to use GATK to identify genomic variants from my .bam file. When I use the command java -jar GenomeAnalysisTK.jar -R chr13.fa -I chr13fixed.bam -o SNP.raw.vcf -T UnifiedGenotyper -standcallconf 30.0 -standemitconf 15.0 -dcov 500 it always return this error: SAM/BAM file SAMFileRead ...
gatk picard file bam written 7.8 years ago by Edoardo Giacopuzzi60 • updated 7.8 years ago by Sean Davis25k

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