User: agata88

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agata88490
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Poland
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16 hours ago
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1 year, 9 months ago
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Posts by agata88

<prev • 228 results • page 1 of 23 • next >
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How to get depth for SNP or indel in vcf file?
... Hi all! Is there a tool that can calculate the coverage for SNP and Indel from VCF and BAM file? I have vcf file from 1000g databse and unfortunately there is NO information about read depth (eg DP). Thank you in advance, Best, Agata PS. here is the line from vcf to prove that information abou ...
vcf written 1 day ago by agata88490
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Comment: C: 1000g database with wrong variant annotation?
... Yes, I know. I am actually using VarScan for variant detection :) Thanks ...
written 2 days ago by agata88490
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Answer: A: SNPs and CNVs Associated with Drug Response
... How about PGMD? As I remember this database store drugs related to SNVs. I think It is not free available (except students?) which might be a problem. https://www.qiagenbioinformatics.com/products/pgmd/ Best, Agata ...
written 2 days ago by agata88490
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Answer: A: What does *.* represent after Ensembl transcript name ?
... It looks like it is a version of transcript, see here: http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000188283;r=19:37226464-37248738;t=ENST00000352998 So I think it is the same transcript since the ENST00000352998.3 is no longer available, Best, Agata ...
written 2 days ago by agata88490
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Comment: C: 1000g database with wrong variant annotation?
... Thanks, I will definitely read that, Best, Agata ...
written 2 days ago by agata88490
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Comment: C: 1000g database with wrong variant annotation?
... I see that I have a lot of snp and indel with AC=0. Which means that it has no different allele but still is annotated in vcf file... that is why I've got confused. When I filtered it looks like everything is good. Now I'm feeling embarrassed because I missed it during analysis...still I hope that t ...
written 2 days ago by agata88490
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Comment: C: 1000g database with wrong variant annotation?
... Sorry, I've made that by mistake... thanks for bringing it back :) ...
written 2 days ago by agata88490
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1000g database with wrong variant annotation?
... Hi all, I wanted to validate my pipeline for SNVs discovery. To do that I've downloaded exome fastq and vcf annotation files for each chromosome from http://www.internationalgenome.org/data-portal/sample/HG00119. At the end I wanted to compare snps and indels in both results only for exonic sequen ...
1000g written 2 days ago by agata88490 • updated 2 days ago by Macspider970
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Comment: C: buffer error bwa
... It turned out that files were corrupted during download. Thanks for your help. Best, Agata ...
written 5 days ago by agata88490
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Comment: C: buffer error bwa
... Thank you very much :) ...
written 5 days ago by agata88490

Latest awards to agata88

Popular Question 10 weeks ago, created a question with more than 1,000 views. For normalization of NGS results
Supporter 7 months ago, voted at least 25 times.
Centurion 8 months ago, created 100 posts.
Scholar 10 months ago, created an answer that has been accepted. For A: Idenity, e value or bitscore ?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Idenity, e value or bitscore ?
Scholar 12 months ago, created an answer that has been accepted. For A: Idenity, e value or bitscore ?

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