We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Input files reference and features have incompatible contigs
I am very new to GATK. i read the paper Curr Protoc Bioinformatics. ; 11(1110): 11.10.1–11.10.33. doi:10.1002/0471250953.bi1110s43 and best practices guide. i want to run whole exom analysis to find high confidence SNP and indels .I am stuck at the BQSR analysis step ( BaseRecalibrator). it shows the error message
Input files reference and features have incompatible contigs: No overlapping contigs found.
i did following steps
1. Download the genome file hg38.fa.gz from UCSC genome.
2.Indexing the reference genome : bwa index hg38.fa
3.Create fasta file index : samtools faidx hg38.fa
5. Create sequence dictionary by java -jar picard.jar CreateSequenceDictionary REFERENCE=hg38.fa OUTPUT=hg38.dict
6. mapping the data to reference : bwa mem -R '@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1' -p hg38.fa R1.fastq R2.fastq > aligned_reads.sam
7. sort my align reads: java -jar picard.jar SortSam INPUT=aligned_reads.sam OUTPUT=sorted_reads.bam SORT_ORDER=coordinate
8. marking duplicates : java -jar picard.jar MarkDuplicates INPUT=sorted_reads.bam OUTPUT=dedup_reads.bam METRICS_FILE=metrics.txt
9. index my markduplicate file : java -jar picard.jar BuildBamIndex INPUT=dedup_reads.bam
10. Download dbSNP from this ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b149_GRCh38p7/VCF/00-All.vcf.gz
11. Download indels from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/other_mapping_resources/Mills_and_1000G_gold_standard.indels.b38.primary_assembly.vcf.gz
12. Run the BaseRecalibrator : java -jar gatk-package-188.8.131.52-local.jar BaseRecalibrator -R hg38.fa -I dedup_reads.bam --known-sites SNP_00-All_GRCh38.vcf --known-sites Mills_and_1000G_gold_standard_indels.vcf -O recal_data.table
it shows the error message to index the SNP_00-All_GRCh38.vcf and indel file
13.i index the file by running this command : java -jar gatk-package-184.108.40.206-local.jar IndexFeatureFile -F SNP_00-All_GRCh38.vcf and java -jar gatk-package-220.127.116.11-local.jar IndexFeatureFile -F Mills_and_1000G_gold_standard_indels.vcf
- After index, again i run the BaseRecalibrator : java -jar gatk-package-18.104.22.168-local.jar BaseRecalibrator -R hg38.fa -I dedup_reads.bam --known-sites SNP_00-All_GRCh38.vcf --known-sites Mills_and_1000G_gold_standard_indels.vcf -O recal_data.table
it shows the error " A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found."
Please help me to solve the problem