ERROR while calling variants...
I am using gatk-4.1.7.0 version with following command, however I am getting error. please advice....
Command:
gatk-4.1.7.0$./gatk HaplotypeCaller -R /home/kumarm/allan-work/RNASEq-alignment/ref_sequence.fasta -I /home/kumarm/allan-work/RNASEq-alignment/sorted-out-align.bam.bai -O /home/kumarm/allan-work/RNASEq-alignment/raw_variants.vcf
ERROR:::
A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
reference contigs = [KF267450.1]
reads contigs = []
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Hi I have fastq (MnION) file and a reference fasta file..I have still issue to not getting results ......
--FILE 1
@ID_5331388
CTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCC
+ID_5331388
AAFFFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJ7FFJJJJJJJJJFJJJFJJJJJJJJJJJJJFJJJJJJJJJJJJJJJ
@ID_6694963
CTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGCTGGGAATTCTCCTCCACTCTGGGATGGGCATTCTCCTCC
+ID_6694963
AAAFFJJJJJJJFJJJJJFJJFJJJJJJJJJJJJJJFJJJF<FJJJJJJJJJ-AJ<-AJF-7JFF7--7<7FFFJJ-<<AA-FF-<FAJ))-AF-----)---FILE 2
>KF267450.1
TTAAAAGAGATTTTCTATCTACGGATAGTTAGCTCTTTTTCTAGACTCTTGTCTACTCAATTCAACTAAA
CGAAATTTTGTCCTTCCGGCCGCATGTCCATGCTGCTGGAAGCTGACGTGGAATTTCATTAGGTTTGCTT--ERROR--
A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
reference contigs = [KF267450.1]
reads contigs = []
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