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Search: Posts Made By: kasthuri
Forum: Bioinformatics 10-19-2014, 03:16 PM
Replies: 1
Views: 807
Posted By kasthuri
Identifying tumor and the corresponding germline

Hi,

I have two .bam files, one of which is a tumor and the other is the corresponding normal/germline from the same patient. Is there an efficient way to identify them correctly,...
Forum: Bioinformatics 05-24-2013, 06:00 AM
Replies: 5
Views: 2,676
Posted By kasthuri
Thank you swbarnes2. I found VariantsToTable in...

Thank you swbarnes2. I found VariantsToTable in GATK does exactly what I wanted.
Forum: Bioinformatics 05-23-2013, 03:55 PM
Replies: 5
Views: 2,676
Posted By kasthuri
Also, I will be just happy with the ALT entries...

Also, I will be just happy with the ALT entries instead of actual variants. Is it possible to get that?

Thanks
-K.
Forum: Bioinformatics 05-23-2013, 03:51 PM
Replies: 5
Views: 2,676
Posted By kasthuri
Thank you, id0. It works and I get the genotypes....

Thank you, id0. It works and I get the genotypes. But I don't get other information from the FORMAT fields. I know I can use --extract-FORMAT-info separately and 'paste' these two lists, but I would...
Forum: Bioinformatics 05-23-2013, 03:03 PM
Replies: 5
Views: 2,676
Posted By kasthuri
Extracting REF and ALT from VCF

This may be a simple question.

I am trying to extract CHR, POS, REF and ALT and other info from a VCF file to a txt file using vcftools. Can somebody point me how to get REF and ALT? I don't get...
Forum: Bioinformatics 02-28-2013, 06:56 AM
Replies: 0
Views: 978
Posted By kasthuri
Protein Domains

Gurus,

I have a list of mutations and I want to see on which domains those mutations are (like kinase, C2, N-terminal, Helicase etc.). And I want them in nice plot like this:
...
Forum: Bioinformatics 01-28-2013, 12:59 PM
Replies: 0
Views: 757
Posted By kasthuri
Pileup Question

Hi,

I am having several bam files and I need to do a pileup of each bam's such that all the pileups have the complete hg19 coordinates. 'samtools mpileup' with all the bams misses certain...
Forum: Bioinformatics 01-17-2012, 06:13 AM
Replies: 2
Views: 1,237
Posted By kasthuri
Thank you swbarnes2. This is great!

Thank you swbarnes2. This is great!
Forum: Bioinformatics 01-16-2012, 09:45 AM
Replies: 2
Views: 1,237
Posted By kasthuri
Whole exomes from whole genome

How do I extract whole exomes from whole genome data? I have a bunch of whole exomes and I just need the exomic part.

Thanks
-Kasthuri
Forum: Bioinformatics 01-13-2012, 11:24 AM
Replies: 1
Views: 950
Posted By kasthuri
Chasm

I have a bunch of mutations with Ensembl annotations for gene name and I am trying to run CHASM:

http://wiki.chasmsoftware.org/index.php/CHASM_Tutorial#Configuration_Options

It requires...
Forum: Bioinformatics 01-12-2012, 10:48 AM
Replies: 3
Views: 2,219
Posted By kasthuri
Thanks! I don't think they have this info in the...

Thanks! I don't think they have this info in the IGV documentation.
Forum: Bioinformatics 01-12-2012, 09:14 AM
Replies: 3
Views: 2,219
Posted By kasthuri
Black line between two reads in IGV

It will be great if somebody can enlighten me on what does a black line between two consecutive reads in IGV, represent? I am attaching a pic. I tried searching but couldn't find any info.

Thanks...
Forum: Bioinformatics 01-12-2012, 03:54 AM
Replies: 2
Views: 1,305
Posted By kasthuri
Great! Thanks. Well, for example, it is samtools...

Great! Thanks. Well, for example, it is samtools faidx filename.fasta chr1:139266-139268 (to make it easy for folks who may have this question in future). Reference fasta should be indexed first...
Forum: Bioinformatics 01-11-2012, 04:39 PM
Replies: 2
Views: 1,305
Posted By kasthuri
Searching bases in reference genome.

Is there a command line tool that would give me the nucleotide before and after a given mutation/variant base?

Thanks
-Kasthuri
Forum: Bioinformatics 01-10-2012, 06:39 PM
Replies: 5
Views: 10,026
Posted By kasthuri
VCF to MAF (Mutation Annotation Format)?

:rolleyes:

Can anybody point me to a tool that can convert a vcf file to Mutation Annotation Format (MAF) file?

That will be great!

Thanks
-Kasthuri
Forum: Bioinformatics 12-30-2011, 12:32 PM
Replies: 2
Views: 2,869
Posted By kasthuri
SnpSift tool is able to query and obtain the...

SnpSift tool is able to query and obtain the lines that matches the query. But I just want the subfield of the EFF. Looks like I may have to do the text processing myself - not too bad though!
...
Forum: Bioinformatics 12-29-2011, 06:44 PM
Replies: 6
Views: 5,059
Posted By kasthuri
I found some of the errors in GATK were gone if I...

I found some of the errors in GATK were gone if I "clean" the bam files using:

samtools view -F 0x04 -b in.bam > out.bam

after this I sort, index and mark the duplicates using Picard before...
Forum: Bioinformatics 12-29-2011, 06:30 PM
Replies: 2
Views: 2,869
Posted By kasthuri
snpEff and extracting EFF field

Hi,
Currently I am using snpEff to annotate vcf files. The output is also a vcf with the info field populated by several annotations including the gene names.

For a sample, I am showing the...
Forum: Bioinformatics 06-29-2011, 09:10 AM
Replies: 7
Views: 7,759
Posted By kasthuri
Thank you for this wonderful suggestion. ANNOVAR...

Thank you for this wonderful suggestion. ANNOVAR is great!
Forum: Bioinformatics 06-29-2011, 08:11 AM
Replies: 7
Views: 7,759
Posted By kasthuri
Thanks ulz_peter, I am looking into this now.

Thanks ulz_peter, I am looking into this now.
Forum: Bioinformatics 06-29-2011, 08:10 AM
Replies: 7
Views: 7,759
Posted By kasthuri
The problem is the shortcut in their folders are...

The problem is the shortcut in their folders are not working on the above mentioned ftp site.
Forum: Bioinformatics 06-28-2011, 04:00 PM
Replies: 7
Views: 7,759
Posted By kasthuri
Annotating VCF files

Can anybody tell me how to annotate vcf files for hg19 aligned file? I tried GATK, vcftools and vcfCodingSnps.

GATK - I couldn't find their refGene file in their ftp server
...
Forum: Bioinformatics 06-26-2011, 06:48 AM
Replies: 1
Views: 2,299
Posted By kasthuri
QUAL vs GQ in GATK

I am trying to do SNP analysis and using GATK's UnifiedGenotyper to call the SNP's. GATK gives me a vcf file in which I find there are both QUAL field and GQ field. As I understand, QUAL field...
Forum: Bioinformatics 06-23-2011, 01:40 PM
Replies: 0
Views: 2,258
Posted By kasthuri
Union of two VCF's in GATK

Hi,

I am using GATK in which I use their 'CombineVariants' to merge two VCF files which might have two different QUAL values. I see that if there are two records at a particular chromosome...
Forum: Bioinformatics 06-14-2011, 03:19 PM
Replies: 3
Views: 2,546
Posted By kasthuri
Thank you fpepin. These are matched normals of 8...

Thank you fpepin. These are matched normals of 8 pairs. I guess I will run them individually as it is advised.
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