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Somehow the requested coordinate is not covered by the read?
I was running some samtools calls through UG with genotyping_mode GENOTYPE_GIVEN_ALLELES after reading this thread:
I got this error message:
##### ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Alignment 440969 | 36S26M1D6M1I2M1D1M3D27M1S
What did I do wrong? It works for most other fragments (chrom20:pos1-pos2). Is it possible to avoid this error message and just do ./. calls at coordinates not covered by reads? I'm not sure, why samtools called at a coordinate not covered by a read. I don't know at which coordinate this happened. I was at this coordinate, when the error happened:
INFO 10:21:06,036 ProgressMeter - 20:479014 2329564.0 55.0 m 23.6 m 0.6% 6.7 d 6.7 d
I was using this command:
vcf=samtools.vcf.gz $java -Djava.io.tmpdir=tmp -Xmx63900m \ -jar $jar \ --analysis_type UnifiedGenotyper \ --reference_sequence $ref \ --input_file bam.list \ --dbsnp $dbsnp138 \ --num_cpu_threads_per_data_thread 3 \ --num_threads 4 \ --out $out \ --intervals $vcf \ -stand_call_conf 10 \ -stand_emit_conf 10 \ --genotype_likelihoods_model BOTH \ --output_mode EMIT_ALL_SITES \ --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest \ --alleles $vcf \ --genotyping_mode GENOTYPE_GIVEN_ALLELES \ -L 20:$pos1-$pos2 \