User: Makplus T
Makplus T • 70
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Posts by Makplus T
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... Agree, the better solution is to provide a target BED from my Sequence platform, but normally, their position infos are similar.
I re-run the CNV-kit with Agilent exon target region.BED, and finally got the similar result with huge CNV size.
I think it maybe the problem happen in determining t ...
written 6 days ago by
Makplus T • 70
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... Hello,
I have some case-match Whole Exome seq samples, and I tried to call CNV event in the case corhot with CNVkit, my code is followed CNVkit manual and parameters are below:
cnvkit.py batch ${all_tumor.bam} --normal ${all_normal.bam} \
--targets ${target_bed} --fasta ${ref_genome} \
...
written 8 days ago by
Makplus T • 70
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... Makes sense.
I provide single sample to samtools mpileup , so I think AF = 0.5 or 1 is the actually the right result. ...
written 4 weeks ago by
Makplus T • 70
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... Thanks Kevin, I think I got the point.
AF in GATK-produced VCF stands for "allele fraction of alternating allele in tumor",
while AF in VCF produced by bcftools means "allele frequency", I think this is a population concept, "allele fraction of alt allele in all samples" . So when I only give on ...
written 4 weeks ago by
Makplus T • 70
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... Thanks for your helpful answer, I would try the approach your mentioned.
But I have some confuse on the reason why we need multi-bam for one sample with different downsample rate ? And why we need downsample in variants calling? In order to reduce something such as data volume, elapsed time, and ...
written 4 weeks ago by
Makplus T • 70
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... Hi,
I have called the mutation in Human NGS data follow the samtools/bcftools mpileup call, and got the VCF files. Due to the false positive, I need to go further filter, just like filter the position with more than 20 reads support, Or the remove the variants frequency less than threshold value, ...
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... Hello,
I have ran the Mutect2 with tumor only mode and get the VCF file, and then I check the mutation site in iGV with a bamout file and my raw bam file from bwa, but I have trouble in explain why Mutect2 only report one position while there are about 4 site obvious .
mycode:
gatk Mutect2 -R ...
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... Yes, you are right. My picture just shows a un-methylation C site and its new chains after PCR. And my confusion is that many blogs say methylation C will keep C and un-methylation C will become a T, but during the PCR , it seems there will generate the un-methylation C. ...
written 9 months ago by
Makplus T • 70
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... Thanks. But sorry for my superficial understanding of methylation sequencing experiment, what puzzles me actually is how the PCR process prevents a new C synthesis, because there is still a G base in the other chains. ...
written 9 months ago by
Makplus T • 70
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... I knew that using bisulfite can turn unmethylated C to U, but I still have a problem about this technology:
Supposed a non-methylated C in the forward chain now becomes U, but then during PCR, with a G in reverse chain, will it re-synthesize the C-base in the new chain (may be something happen jus ...
written 9 months ago by
Makplus T • 70
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For should FASTA files be sorted before indexed with SAMtools?
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For Some symbols share the same ensembl ID in org.Hs.eg.db but not in ensembl website, how to deal with it?
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