Seqanswers Leaderboard Ad



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

  • dpryan
    You can't just reorder the lines in the fai file, they need to be in the exact same order as the contigs in the fasta file.

    You have two options:
    (1) Reorder the fasta file. If there are a LOT of contigs then this could be a pain. The simplest method is to split the fasta file by chromosome and then reconcatenate the proper order.
    (2) Reorder the BAM file. You can use picard tool's ReorderSam command to do this. This will order things to match the fasta file.

    I expect option (2) is easier in your case.

    Leave a comment:

  • GATK RNA-Seq pathway Split 'n' Trim- problems with .bai and .fai index compatibility

    I am processing aligned RNA-Seq data to get phased haplotypes of novel genes in sea stars. I am working through the analysis pipeline that used the Genome Analysis Toolkit suite of software, and is detailed on the Broad Institute website:


    I am up to the Split 'n' Trim stage of the pipeline, where the SplitNCigarReads tool is used to refine the sequence alignment. I have hit some problems with my index files. The order of the scaffolds and contigs for .fai (fasta index file) and .bai (index for bam file; bam file has been sorted, read-groups have been added and duplicated marked) files is different.

    e.g. the .fai file:
    Scaffold1 154793 11 70 71
    Scaffold2 383464 157027 70 71
    Scaffold3 336159 545981 70 71

    eg. the .bai file (samtools idxstats filename.bam):
    Scaffold1 154793 0 0
    Scaffold10 244803 0 0
    Scaffold100 200181 0 0

    I therefore got the following error from GATK:
    ##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
    ##### ERROR reads contigs = [Scaffold1, Scaffold10, Scaffold100, Scaffold1000...
    ##### ERROR reference contigs = [Scaffold1, Scaffold2, Scaffold3, Scaffold4…

    I wrote a script to change the order of the items in the .fai file so they would be in the same order as the .bai file, but this produced another error:
    ##### ERROR MESSAGE: Couldn't read file filename.fa because Mismatch between sequence dictionary fasta index for filename.fa, sequence 'Scaffold2' != 'Scaffold10'.

    Can anyone suggest a good work around for this problem? Do I need to change the order of entries in the fasta file reference sequence? Should I alter the .dict file (scaffolds/contigs are in the same order as they are in the original .fai file)?
    Last edited by gwilymh; 11-17-2014, 06:03 PM. Reason: Specifying the specific part of the pipeline where I had the problem

Latest Articles


  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin

    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM
  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin

    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM





Topics Statistics Last Post
Started by seqadmin, 05-24-2024, 07:15 AM
0 responses
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 10:28 AM
0 responses
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 07:35 AM
0 responses
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
Last Post seqadmin