af-only-gnomad.raw.sites.b37.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
Answered
thanks a lot
If you are seeing an error, please provide(REQUIRED) :
a) The Genome Analysis Toolkit (GATK) v4.2.4.1
b) $gatk Mutect2 -R $ref_fasta -L $result_dir/$sample.bed -I $result_dir/$sample.temp.bam -germline-resource $af_only_gnomad_vcf --native-pair-hmm-threads 96 --f1r2-tar-gz $result_dir/$sample.f1r2.tar.gz -O $result_dir/$sample.unfiltered.vcf:
c) 09:59:23.384 INFO Mutect2 - Initializing engine
09:59:23.748 INFO FeatureManager - Using codec VCFCodec to read file file:////gatk/af-only-gnomad.raw.sites.b37.vcf.gz
09:59:23.852 INFO FeatureManager - Using codec BEDCodec to read file file:////result/align/abc.bed
09:59:23.891 INFO IntervalArgumentCollection - Processing 2272296 bp from intervals
09:59:23.897 WARN IndexUtils - Feature file "file:////gatk/af-only-gnomad.raw.sites.b37.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file:
If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?
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Hi linouhao,
This is not an error, just a warning. Was there an error message other than what you have posted here?
Best,
Genevieve
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thanks a lot. it is a warning, but it mutect2 will stop;
I have to realign the fastq by human_g1k_v37.fasta; though I ever tried to do to make it suitable for af-only-gnomad.raw.sites.b37.vcf.gz
samtools view -h $tumor_bam | sed -e '/^@SQ/s/SN\:chr/SN\:/' -e '/^[^@]/s/\tchr/\t/2' | samtools view -bS - > $result_dir/$sample.temp.bam
samtools index $result_dir/$sample.temp.bam -
linouhao could you paste the entire program log for Mutect2?
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