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Forum: Bioinformatics 01-07-2016, 01:56 AM
Replies: 1
Views: 1,598
Posted By amruta.bn
Hi , I am Bioinformatics enthusiast from...

Hi ,

I am Bioinformatics enthusiast from India.It will be really helpful if you can answer below questions.


1. I have downloaded the vcf files from following link....
Forum: Bioinformatics 01-12-2012, 01:42 AM
Replies: 3
Views: 2,583
Posted By amruta.bn
Hi, I generated the SAM file using bowtie...

Hi,

I generated the SAM file using bowtie version0.12.7 but i am not able to generate a proper bcf file.BCF file is genertaed within 2 minutes and normally it will take time.The commands i gave...
Forum: Bioinformatics 01-06-2012, 12:40 AM
Replies: 4
Views: 3,231
Posted By amruta.bn
##fileformat=VCFv4.1 ##samtoolsVersion=0.1.18...

##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality...
Forum: Bioinformatics 01-05-2012, 03:27 AM
Replies: 3
Views: 2,583
Posted By amruta.bn
Exclamation Is SRA format to vcf conversion possible

Hi,

I am new to SRA format. Can anyone give me an introduction.
I wanted to convert SRA format to vcf format.
I have checked in SRAToolkit. It does not support direct conversion of SRA to VCF....
Forum: Bioinformatics 01-05-2012, 03:22 AM
Replies: 0
Views: 1,401
Posted By amruta.bn
Exclamation Problem with vcf file generated

Hi,

I have generated a vcf file from a bam file and reference sequence using the following command

samtools faidx input.reference.fa
samtools index sortedhg19.bam
samtools mpileup -d 8000...
Forum: Bioinformatics 01-05-2012, 03:11 AM
Replies: 4
Views: 3,231
Posted By amruta.bn
Hi, I have generated a VCF file using the...

Hi,

I have generated a VCF file using the command

samtools faidx input.reference.fa
samtools index sortedhg19.bam
samtools mpileup -d 8000 -uf input.reference.fa my.sortedhg19.bam |...
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