User: petersam

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petersam0
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Posts by petersam

<prev • 4 results • page 1 of 1 • next >
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Filtering phased alleles with GATK
... I am looking for a pathogenic variant with exome sequencing on affected and unaffected related individuals. Initial analysis has not shown any obvious candidates. Im looking to retrieve more information with our existing data set which might support or refute different genome regions. It is a relati ...
linkage gatk exome variants phased written 2.6 years ago by petersam0
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Change vcf header in windows
... I have run into a problem that seems simple but has been surprisingly hard. I have a group of .g.vcf.gz files that I want to joint genotype with GATK. They were generated with incorrect and sloppy read set names. I would like to change the name in the header before grouping them together. Unfortunat ...
vcf gatk header samtools windows written 2.8 years ago by petersam0 • updated 2.8 years ago by Zaag720
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Comment: C: Selecting Variants based on annotations in a VCF file
... Thank you. That was incredibly easy. ...
written 2.8 years ago by petersam0
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Selecting Variants based on annotations in a VCF file
... I have a VCF file generated with GATK and annotated with SNPeff. There is an annotation field described as > ##INFO=C|||||| I have been using GATK SelectVariants to generate variant lists based on sample genotype and quality metrics but would also like to isolate all variants with different ...
vcf gatk snpeff variants written 2.8 years ago by petersam0 • updated 2.8 years ago by Pierre Lindenbaum121k

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