I am using FastaAlterenateReferenceMaker to generate new reference genome using SNPs in .vcf file. I used following command:
java -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R genome.fa -o newgenome.fa -V snps.vcf
I got this error:
##### ERROR MESSAGE: Input files variant and reference have incompatible contigs: The contig order in variant and referenceis not the same; to fix this please see (https://www.broadinstitute.org/gatk/guide/article?id=1328), which describes reordering contigs in BAM and VCF files.
##### ERROR variant contigs = [10, 1, 2, 3, 4, 5, 6, 7, 8, 9, MT, Pt]
##### ERROR reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, MT, Pt]
vfc file contains SNPs for only one genome (ch6) and does not have any contig description line, and using the script in the link didn't work. I tried changing the order of the genome.fa to be same as variant contigs but this time, the chromosomes of the newgenome.fa were wrong (e.g. ch7 had the sequence of ch6, ch1 had the sequence of ch10, etc.)
How can I fix this? Thank you in advance.
I am trying to compute mean coverage (using GATK DepthOfCovearge) for a BAM file (targeting sequencing) aligned using reference hg19.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ucsc.hg19.fasta \ -T DepthOfCoverage \ -I my_bam.list \ -L my_targets.bed \ -o coverage
The problem reported is:
##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths: ##### ERROR contig reads = chrM / 16569 ##### ERROR contig reference = chrM / 16571. ##### ERROR reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM] ##### ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249] ##### ERROR ------------------------------------------------------------------------------------------
Could you please help me to find a solution? Many thanks in advance.
I am running RealignerTargetCreator using GATK version GenomeAnalysisTK-1.2-4-gd9ea764 and I am getting the following error: `
I already checked that I am using the right Reference FASTA file and the correct .bam file, that I have used for alignment before. Therefore, I am clueless why I am getting this error? I would appreciate your help regarding this problem. Any suggestion is welcome?
I am currently trying to run the RealignerTargetCreator on some bam files which were aligned to hg19 howver am getting this error `ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:
After some initial investigation I found that the supplied hg19 reference genome which was being used for mapping was using rCRS mtDNA. other then realigning to a different build of hg19 is there any way to easily fix this problem through GATK?
I'm trying to run some tests and can't because I get this message that my reference is not the same as the input file, even though I've been assured that it is. Is there a way around this? I'm new to this, so step-by-step details would be appreciated, thanks