Announcement

Collapse
No announcement yet.

Generate a SAM file containing aligned reads GATK Error

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Generate a SAM file containing aligned reads GATK Error

    Hello All,
    I am a new bee here and entirely new to bioinformatics, I am working on the tutorial of GATK. I using its command to map and mark duplicates . Here these commands i am using
    bwa mem -M -R "@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1" -p ucsc.hg19.fasta gcat_set_037_2.fastq > aligned_reads.sam

    i am getting this error.
    [bwt_restore_sa] fail to open file 'ucsc.hg19.fasta.sa' : No such file or directory


    Please guide me what i am doing wrong.
    regards

  • #2
    Is ucsc.hg19.fasta in that directory? Is it properly indexed?

    Comment


    • #3
      Yes its in the same folder, I am re indexing it again .

      Comment

      Working...
      X