Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • BWA alignment for multiple genotypes

    Hello expert members,
    I would like to get your advice regarding BWA alignment options. I found in the bwa manual that it uses only two read files for paired-end and one read file for single-end data at a time. However, I have 3 genotypes (each has two fastq files) to identify and compare SNPs among them. According to the BWA guideline, I used two (read1.fastq and read2.fastq) files of one genotype at a time to make alignment against the reference genome using the following command line:

    bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered > aln-BH.sam
    bwa mem ref.fasta Cyp_1.fastq_filtered Cyp_2.fastq_filtered > aln-Cyp.sam
    bwa mem ref.fasta SR_1.fastq_filtered SR_2.fastq_filtered > aln-SR.sam

    Now I have 3 *.sam files for the 3 genotypes for SNPs variant calling. My question - is it possible to use all 6 fastq files from 3 genotypes in the single command to get a single *.sam file like below:

    bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered Cyp_1.fastq_filtered Cyp_2.fastq_filtered SR_1.fastq_filtered SR_1.fastq_filtered > aln-bwa.sam

    Thank you so much for taking your valuable time and I would appreciate your advice.

    Thanks
    Shofi

  • #2
    How to compare vcf file containing snps between two cultivars

    Hi all,
    I have three vcf files containing SNPs of three different cultivars. The SNPs were called using GATK's UnifiedGenotyper program. After stringent filtering with GATK's hard filters, I have approx. approx. 3.5 millions SNPs in the three cultivars. Now I would like to compare between two cultivars based on the vcf files to identify common and specific SNPs in vcf1/vcf2, vcf1/vcf3 and vcf2/vcf3, and also like to generate venn diagram.

    Can anyone suggest me - which tool I can use to identify common and specific SNPs between two cultivars? I do appreciate your help.
    Last edited by shis; 01-21-2017, 09:18 AM.

    Comment


    • #3
      Coincidentally, I just released a program for this purpose, in the BBMap package. You can use it like this:

      Code:
      comparevcf.sh in=sample1.vcf,sample2.vcf out=difference.vcf subtract
      It supports union, intersection, and subtraction. Note that subtraction is order-dependent while the other operations are not.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X