User: ari.nazarian

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ari.nazarian10
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Posts by ari.nazarian

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Difference in the following reference genomes, both from Broad Institute FTP?
... I did some alignment and BQSR using the Homo_sapiens_assembly19.fasta that I found at ftp://ftp.broadinstitute.org/pub/seq/references. I only later discovered the GATK resource bundle at ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/ and the human_g1k_v37_decoy.fasta found there. Ri ...
assembly alignment reference written 2.8 years ago by ari.nazarian10
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BQSR on one sample vs. all samples in a run
... I'm trying to run BQSR on a sample from a miSeq run, but received an error saying that I need to add read groups. Since this sample was one of 40-something samples multiplexed during a run, should I merge all the samples on one BAM before running BQSR, so that BQSR is more accurate/effective? I read ...
bsqr miseq written 2.9 years ago by ari.nazarian10 • updated 2.9 years ago by cpad011212k
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Comment: C: Merging VCFs: Illumina/GATK and LoFreq
... I've just run into so many different errors that I was hoping I didn't have to go into the weeds but here's a brief overview of the initial issue I'm having (not even considering the errors when I try to manipulate the vcfs, like adding columns with sed and so forth: I ran vcf-merge on two vcfs, on ...
written 2.9 years ago by ari.nazarian10
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Merging VCFs: Illumina/GATK and LoFreq
... I have VCFs from a number of different tumor samples sourced mostly from two different variant callers that I'm trying to merge onto one sheet: GATK (via an Illumina MiSeq machine) and LoFreq. The end goal is to upload the merged VCF to CRAVAT for easier visualization/interpretation of variant infor ...
variant calling vcf miseq written 2.9 years ago by ari.nazarian10
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Comment: C: "No space left on device" after "Finished constructing BWT"
... That's rough.Thanks for the input, I thought maybe cause my FASTQ's were small files (5MB for each paired-end file) that this might work out. Ok, well how about indexing itself? It seems as if indexing is still something I should be able to complete on my machine, no? ...
written 3.0 years ago by ari.nazarian10
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"No space left on device" after "Finished constructing BWT"
... This is my first time trying out a fastq -> VCF pipeline, so I don't have the experience to be able to determine if things are working as I'm chugging through each step (from trimming, to alignment, to variant calling). I just tried to create an index using hg19.fa on my MacBook Air which has 4 ...
assembly bwa rna-seq written 3.0 years ago by ari.nazarian10 • updated 3.0 years ago by mforde841.2k

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