User: ambi1999

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ambi199920
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Posts by ambi1999

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New Fasta Sequence From Variant Calls File
... Hi, Is there a way in Galaxy to create a new FASTA reference sequence from a reference sequence and vcf file? Sometime similar to GATK FastaAlternateReferenceMaker. Cheers, Ambi. ...
vcf fasta written 13 months ago by ambi199920
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empty QUAL filed in Naive Variant caller vcf output
... Hi, The QUAL field in vcf output of Naive Variant Caller is empty for all the variants. Any reason? Attached is screenshot of the vcf. I will email my galaxy history link to galaxy-bugs@lists.galaxyproject.org, and include a link to this post so you can associate the two. Note: I do get QUAL val ...
variant caller vcf qual naive variant caller written 14 months ago by ambi199920
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Subtract one VCF file from another VCF file
... Hi, Is there a way in Galaxy to subtract one VCF file from another to get a VCF file containing just the SNPs unique to one of the samples? I have tried Subtract Whole Dataset under 'Join, Subtract and Group' but it does not seem to work give me the correct answer. ps: I know subtract in bedtool ...
vcf snp written 14 months ago by ambi199920 • updated 14 months ago by Jennifer Hillman Jackson23k

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