User: drkennetz

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drkennetz500
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Posts by drkennetz

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Comment: C: How to filter a VCF file with a list of CHR or contig IDs?
... Oh, that's a good point I didn't really think of! I think rather than catting you'd need to join them back together with some tool that understands the vcf format, like bcftools. Thanks! ...
written 4 months ago by drkennetz500
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Answer: A: How to filter a VCF file with a list of CHR or contig IDs?
... If you had one contig per line (I'll call it contigs.txt) you could do a simple bash script using what you posted above: cat contigs.txt | while read CONTIG; do vcftools --vcf TotalRawSNPs.vcf --chr $CONTIG --recode --recode-INFO-all --out $CONTIG.out done cat *.out >& ...
written 4 months ago by drkennetz500
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MarkDuplicates of a queryname sorted bam more expensive than a coordinate sorted bam
... Hi all, I am currently aligning/sorting some DNA data (WGS, WES) with high depth. I have performed gatk SortSam using SORT_ORDER="queryname" prior to marking duplicates ultimately because of consistency of output results. When I coordinate sort and then mark duplicates, I commonly see situations wh ...
next-gen alignment written 6 months ago by drkennetz500
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Comment: C: CWL - glob an array of output files based on a single input string
... Thanks, I have posted there but I am currently on hold of being approved by a moderator. I will delete this if my post gets approved. I appreciate the redirect! ...
written 7 months ago by drkennetz500
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Comment: C: CWL - glob an array of output files based on a single input string
... Ah thanks, should I delete the post? ...
written 7 months ago by drkennetz500
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CWL - glob an array of output files based on a single input string
... Hi all, I am writing a CWL command line tool for fastp which has the option to take an input fastq or fastq pair and split each fastq by number of lines which is beneficial for an embarrassingly parallel workflow. So I want to write a tool that has the option to require fastq1 as input, but also opt ...
cwl written 7 months ago by drkennetz500
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Comment: C: Divine tool configuration file requirments
... This would probably be better served as an issue on their github repository. ...
written 9 months ago by drkennetz500
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Comment: C: What were the most impactful Bioinformatics papers published this year
... Ain't no shame in his game! Haha. ...
written 10 months ago by drkennetz500
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Answer: A: Python FASTA scripting
... You can do the following: import sys def fasta_parser(fasta): """ Iterates through fasta Args: fasta (file): fasta_file Returns: seqs (list): list of seqs headers (list): list of headers """ seqs = [] ...
written 13 months ago by drkennetz500
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Answer: A: How to automate bcl2fastq such that it is launched every time the run finishes o
... I wrote a more generalized shell script back in the day to do the same. It actually just runs `stat` on the directory which displays the status of a file or filesystem. I did stat rather than looking for a file because locally we transfer our data from the sequencer to an hpc filesystem and sometime ...
written 13 months ago by drkennetz500

Latest awards to drkennetz

Scholar 3 months ago, created an answer that has been accepted. For A: CommandLineTool doesn't finish
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: CommandLineTool doesn't finish
Appreciated 13 months ago, created a post with more than 5 votes. For A: How to count the total aligned bases in BAM?
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Scholar 2.3 years ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
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Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?

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