I am trying to use the -L option of GATK HaplotypeCaller to call SNPs and short InDels with in an interval list. My interval list file (top8snp.interval_list) content is as follows:
12 33029845 33030845 + rs24767598
13 40586682 40587682 + rs24748362
18 24373857 24374857 + rs8856159
21 50381146 50382146 + rs8905059
31 24929114 24930114 + rs23686011
33 18169455 18170455 + rs9197329
35 14265916 14266916 + rs23883139
38 6688818 6689818 + rs24017102
The command I used to call variants is: java -Xmx4g -XX:ParallelGCThreads=1 -XX:ConcGCThreads=1 -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /mnt/software/kit/unicall.kit/gatk-local.jar HaplotypeCaller --native-pair-hmm-threads 1 -R /home/mzhao/data/share/dog_ref/genome/Canis_lupus_familiaris-GCA_014441545.1-unmasked.fa -I IG001_1blood_healthy.dedup.bam -O IG001_1blood_healthy.top8snp.vcf -L ../top8snp.interval_list 2>IG001_1blood_healthyHaplotypeCaller.raw.top8snp.log &
This gives me no SNP or InDel call.
As I know there are SNPs in these regions, I checked the log file. It has the following warnings:
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 12:33029845-33030845 + rs24767598
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 13:40586682-40587682 + rs24748362
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 18:24373857-24374857 + rs8856159
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 21:50381146-50382146 + rs8905059
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 31:24929114-24930114 + rs23686011
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 33:18169455-18170455 + rs9197329
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 35:14265916-14266916 + rs23883139
WARNING 2022-01-28 15:47:14 IntervalListCodec Ignoring interval for unknown reference: 38:6688818-6689818 + rs24017102
May I ask how should I fix this problem?
Many thanks.
