Hi Everyone,

I recently heard about the genome in a bottle project.

I found raw fastq data for NA12878 samples from their GitHub repository. Now I'm trying to reproduce their analysis.

https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/NA12878/sequence.index.NA12878_Illumina_HiSeq_Exome_Garvan_fastq_09252015

I would like to know if it's available a reference code to compare my pipeline (not only the final result but the code).

Thank you in advance,

AY
Hi Yussab, 
as you did not replay, so i do not know what are you planning to do exactly.
it seems that you do have your own pipeline which mean you have the final VCF where it's generated from NA12878.
i know these 2 tools to compare you result with GIAB Data set. (I do not know if there is something else available)

1- Hap.py (https://github.com/Illumina/hap.py):

    hap.py truth.vcf query.vcf -f confident.bed -o output_prefix -r reference.fa

2-RTG tools (https://github.com/RealTimeGenomics/rtg-tools):

generate SDF file from Fasta file (Your reference):

    rtg format "Your_Fasta_File".fasta -o "File_Name_ToOut_Put_Result"

Compare the tow VCF file:

    rtg vcfeval -b  truth.vcf -c query.vcf -o Directary_To_OUTPUT_THE_RESULT -t PATH_TO_SDF_FILE -e GIAB_BED_FILE.bed  --region= Your_Bed_File.bed

I highly recommend you to read the tools manual for better understanding.



