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Search: Posts Made By: bioinf newbie
Forum: Illumina/Solexa 11-01-2016, 01:09 AM
Replies: 1
Views: 1,644
Posted By bioinf newbie
Variants called using GATK from samples of Nextera and TruSeq exome enrichment kits

I am doing variant calling for exomes generated from Illumina HiSeq 2000, with Nextera Exome Enrichment kit.
Earlier I used the same variant calling pipeline to call variants from sequences based...
Forum: Bioinformatics 11-20-2012, 11:14 PM
Replies: 0
Views: 2,235
Posted By bioinf newbie
GATK LiftOverVariants input vcf

Hi,
I am trying to convert a vcf file of b36 build to hg19.
First few line of my vcf file:

##fileformat=VCFv4.0
##INFO=<ID=Database,Number=1,Type=String,Description="Database identifier">...
Forum: Bioinformatics 10-14-2012, 11:55 PM
Replies: 1
Views: 1,788
Posted By bioinf newbie
Hi 1. If you are going with a standard tool...

Hi
1. If you are going with a standard tool like GATK they have specifications and a resource bundle: http://gatkforums.broadinstitute.org/discussion/1215/how-can-i-access-the-gsa-public-ftp-server...
Forum: Bioinformatics 10-14-2012, 04:12 AM
Replies: 12
Views: 4,787
Posted By bioinf newbie
got it figured out. looks like it was my...

got it figured out. looks like it was my ref.fa.fai that was "corrupted". the one i was using was downloaded from a site. generated a new index file for reference. all is well.
many thanks for the...
Forum: Bioinformatics 10-11-2012, 05:19 AM
Replies: 12
Views: 4,787
Posted By bioinf newbie
yes, i tried pileup from samtools version 0.1.15 ...

yes, i tried pileup from samtools version 0.1.15
no change in output..
[afs] 0:0.000
[root@B samtools-0.1.15]#
Forum: Bioinformatics 10-11-2012, 05:09 AM
Replies: 12
Views: 4,787
Posted By bioinf newbie
This is strange! I had the same sample aligned...

This is strange!
I had the same sample aligned using bowtie2 and bwa.
For the bowtie aligned sample, mpileup works well..
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to...
Forum: Bioinformatics 10-09-2012, 11:19 PM
Replies: 12
Views: 4,787
Posted By bioinf newbie
The output from mpileup is empty. The command...

The output from mpileup is empty.
The command I gave for mpileup is :
[root@B Picard_processed]# samtools mpileup -uf /mnt/data/Genomics/Gaurav/Genome/Broad_Homo_sapiens_assembly19.fasta...
Forum: Bioinformatics 10-08-2012, 09:53 PM
Replies: 12
Views: 4,787
Posted By bioinf newbie
Samtools mpileup

I am using samtools mpileup on my data.
I have used bwa for alignment of my NGS whole genome:
bwa sampe ref.fa read?.sai read?.fq.gz > aln.sam
After conversion to bam, and sorting using...
Forum: Bioinformatics 09-18-2012, 11:05 PM
Replies: 1
Views: 1,659
Posted By bioinf newbie
Validate SNP calls from NGS sequencing data with genotying array

How can I validate SNP calls made on my NGS whole genome sequence data with a genotyping array such as Illumina OmniExpress?
Forum: Bioinformatics 09-15-2012, 11:48 PM
Replies: 0
Views: 1,235
Posted By bioinf newbie
Comparison of Genome Sequencing and Array-Based Genotyping

Hi
I have NGS data for several whole genome sequences and I want to determine the accuracy of base calling by comparing the variants with those present in Illumina OmniExpress BeadChip Array for the...
Forum: Bioinformatics 07-10-2012, 01:11 AM
Replies: 2
Views: 2,367
Posted By bioinf newbie
How to compute percentage of my genome covering human reference genome?

I have the alignment file for my genome (bam).
I want to find out % of genome that covered reference human genome with atleast 1 read, 2 reads, 3 reads, and 4 reads.
How do I go about it?
Forum: Bioinformatics 02-15-2012, 08:36 PM
Replies: 5
Views: 12,528
Posted By bioinf newbie
Thank you very much Richard and @twaddlac. :)

Thank you very much Richard and @twaddlac. :)
Forum: Bioinformatics 02-15-2012, 11:58 AM
Replies: 5
Views: 12,528
Posted By bioinf newbie
Genome coverage

How do you calculate the genome coverage for a sequenced genome?
I have the BAM file for my genome, and I have calculated the read depth at each position using samtools depth command.
Is there a...
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