User: mhmtgenc85

gravatar for mhmtgenc85
mhmtgenc8530
Reputation:
30
Status:
New User
Location:
Turkey
Last seen:
2 days ago
Joined:
3 years, 2 months ago
Email:
m*********@gmail.com

Posts by mhmtgenc85

<prev • 39 results • page 1 of 4 • next >
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How to get a report like stuff of a bam file how many percent of the exons are coverred?
... Dear Collegues, Lets say I have a miseq run and have the .bam file from the squencer and I would like to know how many percent of the exons (specific genes) are coverred in these .bam files? Is it possible? Thanks in advance ...
ngs bam miseq exon written 2 days ago by mhmtgenc8530 • updated 2 days ago by WouterDeCoster30k
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Comment: C: How to Get only one annotation with the SnpEff annotation?
... Yeah you are right but for some reason I only would like to get only the first annotation. :) ...
written 5 days ago by mhmtgenc8530
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How to Get only one annotation with the SnpEff annotation?
... Dear All, As you know when annotationg a vcf file each line might have more than one annotation but I would like to get only one annotation for a line? the first one only if possible. So thanks in advance. ...
annotation variation snpeff snp written 6 days ago by mhmtgenc8530 • updated 5 days ago by Pierre Lindenbaum110k
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How to get all variants in original BAM file with HaplotypeCaller? (No correction and BAMout)
... Dear All, As you know when we use HaplotypeCaller in the variant calling pipeline, the script makes corrections and focuses on the true positive variants. and eliminates many vairant so called wrong one or caused by the artifact sequencing. But no matter what I would like to get all the variants co ...
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Comment: C: Is there a way to save a specific Gene in IGV of a whole exome sample?
... Thank you for the tip. I tried it and get the BAM file. But now I need to get the index file of the bam. When I use samtools index test.bam > test.bai I get an error like this EOF marker is absent. invalid BAM binary header (this is not a BAM file) Invalid BAM header. Fail to index.. I have ...
written 7 weeks ago by mhmtgenc8530
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Is there a way to save a specific Gene in IGV of a whole exome sample?
... Dear all, Is there a way to save a specific Gene in IGV of a whole exome sample? For example I have the whole exome sequencing of a sample but I would like to view and save only one gene out of that whole BAM as only one gene specific BAM? Thanks in advance ...
sequence bam igv written 7 weeks ago by mhmtgenc8530 • updated 7 weeks ago by sacha1.3k
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Comment: C: No mutations in BAM (IGV) but a mutation in final VCF?
... Here is another screenshot with detatiled INFO column :) ...
written 3 months ago by mhmtgenc8530
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Comment: C: No mutations in BAM (IGV) but a mutation in final VCF?
... Dear genomax and Ram thanks for the detailed expanation, And finswimmer, here is the IGV image the top one is the original Bam and the bottom one is the bamout produced by Haplotypecaller. And this is the VCF secreenshot; ...
written 3 months ago by mhmtgenc8530
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Comment: C: No mutations in BAM (IGV) but a mutation in final VCF?
... I am trying but having problems on uploading images :( ...
written 3 months ago by mhmtgenc8530
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No mutations in BAM (IGV) but a mutation in final VCF?
... I use GATK 4.0 for the variant calling pipeline. my steps involve MarkDuplicates, BaseRecalibration, ApplyBaseRecalibration and HaplotypeCaller. When I check in a loci there is no mutation in the original BAM file in IGV, but there is a mutation in final VCF and when I check the bamout of the Haplot ...
variant calling gatk haplotypecaller bam igv written 3 months ago by mhmtgenc8530 • updated 3 months ago by WouterDeCoster30k

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Popular Question 22 days ago, created a question with more than 1,000 views. For Does anyone use Python for variant calling?
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Popular Question 9 months ago, created a question with more than 1,000 views. For Does anyone use Python for variant calling?

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