User: Richard

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Richard550
Reputation:
550
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Location:
Canada
Last seen:
2 weeks, 4 days ago
Joined:
7 years ago
Email:
r****************@gmail.com

Posts by Richard

<prev • 89 results • page 1 of 9 • next >
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Comment: C: beginner snakemake scatter gather help
... Thanks Jeremy, For the directory command, I was hoping to create a folder to hold the smaller VCF files per sample. That way it keeps all the files for each sample separate. For example, I have the following in "input" bam1.bam bam2.bam bam3.bam For each of the bam files I wanted to create a fo ...
written 23 days ago by Richard550
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Comment: C: beginner snakemake scatter gather help
... Great! That seemed to help. Now it looks like I'm struggling to understand the wildcards. In the code below I want to process each BAM files in the folder "input/" to create 1 final VCF per BAM file. My current error is "RuleException in line 7 of /projects/rcorbettprj2/GATK4.0.10_snakemake/S ...
written 23 days ago by Richard550
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Comment: A: beginner snakemake scatter gather help
... Based on the tutorial page suggested above I got this far, but am now getting "SyntaxError in line 13 of Snakefile: invalid syntax" Errors. I suspect it is due to my use of quotes in the shell command. I'm not really sure I'm on the right track so please send along any suggestions. thanks RIchar ...
written 24 days ago by Richard550
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beginner snakemake scatter gather help
... Hi folks, I usually use bash scripts to get things done, and I an going to try my hand at setting up some snakemake scripts to see if I can improve some automation and tracking for some currently ad-hoc analyses. I've gone through the examples on this page: https://snakemake.readthedocs.io/en/stab ...
snakemake written 24 days ago by Richard550
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MD tags - important for analysis tools?
... Hi folks, We have thousands of BAM files aligned with BWA 0.7.6a that we now want to compress with CRAM. We're noticing that a subset of aligned reads will have a different MD tag after CRAM compression/decompression than they had in the original file. The differences seem to be that some se ...
bam md written 7 weeks ago by Richard550
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Comment: C: how to fix old VCF headers
... This seems to get me around the errors, but certainly isn't the best option cat my.vcf | sed 's/PL,Number=-1/PL,Number=A/' | sed 's/Number=0/Number=A/' > myClean.vcf ...
written 5 months ago by Richard550 • updated 5 months ago by finswimmer11k
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how to fix old VCF headers
... Hi folks, I'm working with some older VCF files and trying to get them to work with new Picard and GATK commands. I'm running in to a lot of these sorts of errors... > Unable to parse header with error: Invalid count number, with fixed > count the number should be 1 or higher: key=INFO name ...
vcf written 5 months ago by Richard550
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Human Promethion data available?
... Hi folks, Does anyone know where one can access some example human promethion data? thanks, RIchard ...
sequence written 5 months ago by Richard550 • updated 5 months ago by WouterDeCoster37k
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Germline genome ground truth sets
... Hi all, Apart from the wonderful work done by Genome in a Bottle on the NA12878 cell line, are there any other cells lines out there that provide good ground truth for germline testing? We're interested in SNVs, indels, CNVs, and SVs. Extra points if the ground truth set is for a blood cell line ...
ground truth written 8 months ago by Richard550 • updated 6 months ago by Biostar ♦♦ 20
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merge aligned read pairs that overlap - keep the bases that match the reference
... Hi all, I have aligned paired-end genome data that was sequenced with 150bp reads. The average insert size is just 200bp so there are lots of read pairs with significant overlap of their alignments. I see that there are lots of tools for merging fastq data and at least one that clips overlapping ...
illumina paired-end written 9 months ago by Richard550

Latest awards to Richard

Popular Question 5 months ago, created a question with more than 1,000 views. For STR (short tandem repeats) ID from bam file?
Popular Question 5 months ago, created a question with more than 1,000 views. For Affy 500K positions in hg38
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Popular Question 5 months ago, created a question with more than 1,000 views. For variant calling on amplicon data
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Popular Question 10 months ago, created a question with more than 1,000 views. For variant calling on amplicon data
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Appreciated 14 months ago, created a post with more than 5 votes. For A: Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 14 months ago, created a question with more than 1,000 views. For variant calling on amplicon data
Popular Question 14 months ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 14 months ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
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Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 2.1 years ago, created a question with more than 1,000 views. For variant calling on amplicon data
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Mate Pair Alignment Summary
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Blast Indel Calibration
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Coverage In Bam Alignment
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
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