GATK is throwing an error when using dbsnp hg19 or GCRCh 38 build 156

Question

[Karibu]

I have procesed the dbsnp build 156 as follows;

   1. Edited the Type tags to String instead of integer  both in hg19 and hg38 version to avoid problem related to INFO/RS.

         2. Prepared the new chr number 

    awk -v RS="(\r)?\n" 'BEGIN { FS="\t" } !/^#/ { if ($10 != "na") print $7,$10; else print $10,$5 }' GCF_000001405.25_GRCh37.p13_assembly_report.txt > dbSNP-to-UCSC-GRCh37.p13.map

         3. Remove chr with

        sed -i  's/chr//' dbSNP-hg19.map

         4. updated the chr name with 

    bcftools annotate --rename-chrs dbSNP-hg19.map GCF_000001405.25.bcf   | awk '/^#/ && !/^##contig=/ { print } !/^#/ { if( $1!="na" ) print }' | bgzip -c > dbSNP153.hg19.vcf.gz   

         5. Indexed the file

        tabix dbSNP153.hg19.vcf.gz.

The chromosome naming in my VCF is the same as in the dbSNP database: 1, 2...22, X, Y, MT.

When I run GATK WGS collectMetrics i always get this error(below). What could the issue with dbsnp 156.

I tried the same run with dbsnps 138. Everything went well.

I would appreciate to get your assistance on this issue.

Thank you very much.

Error Message

[Fri Dec 27 19:10:01 JST 2024] picard.vcf.CollectVariantCallingMetrics done. Elapsed time: 25.36 minutes. Runtime.totalMemory()=1447034880 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp java.lang.NullPointerException: Cannot invoke "htsjdk.samtools.SAMSequenceRecord.getSequenceLength()" because the return value of "htsjdk.samtools.SAMSequenceDictionary.getSequence(String)" is null at picard.util.DbSnpBitSetUtil.loadVcf(DbSnpBitSetUtil.java:235) at picard.util.DbSnpBitSetUtil.createSnpAndIndelBitSets(DbSnpBitSetUtil.java:203) at picard.vcf.CollectVariantCallingMetrics.doWork(CollectVariantCallingMetrics.java:110) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289) at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)

[Pierre Lindenbaum]

what is the output of

diff <(tabix -l dbSNP153.hg19.vcf.gz ) <(tabix -l variants.vcf.gz)