Input files reference and features have incompatible contigs

Hi
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-4.0.0.0-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-4.0.0.0-local.jar IndexFeatureFile -F SNP_00-All_GRCh38.vcf and java -jar gatk-package-4.0.0.0-local.jar IndexFeatureFile -F Mills_and_1000G_gold_standard_indels.vcf

  1. After index, again i run the BaseRecalibrator : java -jar gatk-package-4.0.0.0-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

Best Answer

Answers

Sign In or Register to comment.