Variant calling using GATK::ERROR

Question

[Kumar]

Dear All,

I am working to setup pipelines for variants calling. I used SOAPnuke, HISAT, for pre-process. Finally, I am using GATK to call snps/variants. I have tried a lot to figure out my error, please advice........

Here is my process:

1. Removing adaptors and cleaning other parts using SOAPnuke

   ../SOAPnuke filter -l 10 -q 0.5 -n 0.05 -1 trt-unassembled.fastq -C clean_trt.fastq -o result -T 8

2. Index and alignment with hisat2-2.2.0

   ./hisat2-build ..sequence.fastq ../PEDV

   ./hisat2 -x ../PEDV -U ../try.fastq -S ../trt.sam

3. SAM to BAM

   samtools view -Sb ../trt.sam >../trt.bam

   samtools sort ../trt.bam >../sorted-trt.bam

   samtools index ../sorted-trt.bam

4. making .dict and .fai

   java -jar picard.jar CreateSequenceDictionary R= ../sequence.fasta O= ../sequence.dict

   samtools faidx ../sequence.fasta

5. SNPs Calling using GATK

   ./gatk HaplotypeCaller -R ../sequence.fasta -I ../sorted-trt.bam.bai -O ../variants-trt.vcf

-------ERROR: A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found. reference contigs = [LGE3336] reads contigs = []

[Kumar]

Here is the .dict file content:

@HD VN:1.5
@SQ SN:KF267450.1   LN:28038    M5:96f71e94736a55d625aba2a04a7d0e11 UR:file:/home/kumarm/allan-work/bowtie2-trt/sequence.fasta

.fai file content

KF267450.1  28038   12  70  71

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

Answer 1

[JC]

./gatk HaplotypeCaller -R ../sequence.fasta -I ../sorted-trt.bam.bai -O ../variants-trt.vcf

is not sorted-trt.bam? the *bai file is the index

Answer 2

[Pierre Lindenbaum]

try -I ../sorted-trt.bam instead of -I ../sorted-trt.bam.bai