User: mark.rose

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mark.rose10
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United States
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20 hours ago
Joined:
2 years, 6 months ago
Email:
m********@syngenta.com

Posts by mark.rose

<prev • 40 results • page 1 of 4 • next >
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Comment: C: INDEL left alignment in bam and vcf
... Hey Brian Thanks for the suggestion. Worked like a charm. Will look more into the bbmap package. Mark ...
written 6 days ago by mark.rose10
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INDEL left alignment in bam and vcf
... Hello I am performing alignments of amplicons against a reference. Many of these amplicons have sizeable deletions. When aligning reads with such deletions, some aligners (bowtie2, bwa) soft clip the reads or fail to align them. Others, like blasr, produce an alignment which successfully spans the ...
indel aligner bowtie bwa blasr written 10 days ago by mark.rose10 • updated 10 days ago by Brian Bushnell9.6k
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Comment: C: BG7 usage for bacterial genome annotation
... Yes, I've seen these papers. The first one is more practical in that it purports to describe how to execute BG7. That's where I run into trouble. In what I have downloaded from github, there is no executable called "BG7", only "bg7", which is a shell script and does take any of the commands (crea ...
written 12 weeks ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... Should have included the lofreq vcf #CHROM POS ID REF ALT QUAL FILTER INFO ZmpylD 167 . G C 1261 PASS DP=193;AF=0.305699;SB=0;DP4=134,0,59,0 ZmpylD 168 . A T 1315 PASS DP=193;AF=0.305699;SB=0;DP4=134,0,59,0 ...
written 12 weeks ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... Yes, preprocessing the bam file with lofreq indelqual did the trick. Thanks a lot. Still toying with the idea of calling variants on an individual read level though, then setting thresholds on frequency to eliminate sequencing error. The main advantage of doing this, now that the multi-allelic va ...
written 12 weeks ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... Tried this as you suggested $ ~/BioInfo/bin/lofreq_star-2.1.2/bin/lofreq call --no-baq --call-indels -f my_ref.fa my.bam ##fileformat=VCFv4.0 ##fileDate=20161122 ##source=/SD5/people/rosema1/BioInfo/bin/lofreq_star-2.1.2/bin/lofreq call --no-baq --call-indels -f my_ref.fa my.bam ...
written 12 weeks ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... there is only the one ...
written 12 weeks ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... So if you are correct that varscan is calling only the most common variant at each locus, whether you use mpileupcns or mpileupindel, then it is not useful as I have tried to use it since multiple alleles per locus will be common in my data. Likewise for freebayes. If these tools are inadequate (a ...
written 12 weeks ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... the mpileupcns vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 ZmpylD 167 . G C . PASS ADP=193;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:200:193:193:134:59:30.57%:9.0798E-21:32:35: ...
written 12 weeks ago by mark.rose10
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BG7 usage for bacterial genome annotation
... Hi All Is anyone regularly using BG7 for bacterial genome annotation? I'm not seeing many posts on it and, having downloaded it and tried to run it on the included test data, ran into several execution script errors which I think would have been fixed if it were being widely used. It's strategy i ...
annotation tools assembly written 12 weeks ago by mark.rose10

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Popular Question 2.0 years ago, created a question with more than 1,000 views. For unexpected bowtie2 unpaired alignment behavior

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