User: Makplus T

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Makplus T70
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Posts by Makplus T

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Getting huge size of CNV region from CNV-kit with hybrid data.
... 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 T70
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Getting huge size of CNV region from CNV-kit with hybrid data.
... 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} \ ...
cnvkit wes cnv written 8 days ago by Makplus T70
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Comment: C: Confused about the AF tag in VCF from samtools/bcftools mpileup
... 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 T70
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Comment: C: Confused about the AF tag in VCF from samtools/bcftools mpileup
... 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 T70
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Comment: C: How to explain that mutations called by Mutect2 are inconsistent with what I saw
... 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 T70
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Confused about the AF tag in VCF from samtools/bcftools mpileup
... 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, ...
vcf gatk samtools af variants written 4 weeks ago by Makplus T70 • updated 4 weeks ago by Renesh1.9k
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How to explain that mutations called by Mutect2 are inconsistent with what I saw in iGV?
... 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 ...
gatk igv mutation mutect2 written 4 weeks ago by Makplus T70 • updated 19 days ago by davidben20
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Comment: C: will C-base re-synthesize during PCR in Bisulfite methylation sequence
... 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 T70
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Comment: C: will C-base re-synthesize during PCR in Bisulfite methylation sequence
... 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 T70
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will C-base re-synthesize during PCR in Bisulfite methylation sequence
... 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 ...
methylation bisulfite written 9 months ago by Makplus T70

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Popular Question 9 months ago, created a question with more than 1,000 views. For should FASTA files be sorted before indexed with SAMtools?

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