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Potential bug(?) using Picard's sortvcf

mattqdeanmattqdean CAMember Posts: 10
edited February 2016 in Ask the GATK team

I tried sorting my COSMIC vcf using Picard's SortVcf function to match my reference dictionary order. This was after an error using MuTect2 and visiting a provided link.

Command:
java -jar -Xmx32g /cm/shared/apps/picard/1.127/picard.jar SortVcf I=/work/gencode/CosmicCodingMuts.vcf O=/work/gencode/CosmicCodingMuts%.vcf SEQUENCE_DICTIONARY=/work/gencode/GRCh38.p5.genome.dict

Reference dictionary:
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:248956422 M5:2648ae1bacce4ec4b6cf337dcae37816 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr2 LN:242193529 M5:4bb4f82880a14111eb7327169ffb729b UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr3 LN:198295559 M5:a48af509898d3736ba95dc0912c0b461 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr4 LN:190214555 M5:3210fecf1eb92d5489da4346b3fddc6e UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr5 LN:181538259 M5:f7f05fb7ceea78cbc32ce652c540ff2d UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr6 LN:170805979 M5:6a48dfa97e854e3c6f186c8ff973f7dd UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr7 LN:159345973 M5:94eef2b96fd5a7c8db162c8c74378039 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr8 LN:145138636 M5:c67955b5f7815a9a1edfaa15893d3616 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr9 LN:138394717 M5:addd2795560986b7491c40b1faa3978a UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr10 LN:133797422 M5:907112d17fcb73bcab1ed1c72b97ce68 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr11 LN:135086622 M5:1511375dc2dd1b633af8cf439ae90cec UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr12 LN:133275309 M5:e81e16d3f44337034695a29b97708fce UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr13 LN:114364328 M5:17dab79b963ccd8e7377cef59a54fe1c UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr14 LN:107043718 M5:acbd9552c059d9b403e75ed26c1ce5bc UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr15 LN:101991189 M5:f036bd11158407596ca6bf3581454706 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr16 LN:90338345 M5:24e7cabfba3548a2bb4dff582b9ee870 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr17 LN:83257441 M5:a8499ca51d6fb77332c2d242923994eb UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr18 LN:80373285 M5:11eeaa801f6b0e2e36a1138616b8ee9a UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr19 LN:58617616 M5:b0eba2c7bb5c953d1e06a508b5e487de UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr20 LN:64444167 M5:b18e6c531b0bd70e949a7fc20859cb01 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr21 LN:46709983 M5:2f45a3455007b7e271509161e52954a9 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chr22 LN:50818468 M5:221733a2a15e2de66d33e73d126c5109 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chrX LN:156040895 M5:49527016a48497d9d1cbd8e4a9049bd3 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chrY LN:57227415 M5:b2b7e6369564d89059e763cd6e736837 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:GL000008.2 LN:209709 M5:a999388c587908f80406444cebe80ba3 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:GL000009.2 LN:201709 M5:862f555045546733591ff7ab15bcecbe UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:GL000194.1 LN:191469 M5:6ac8f815bf8e845bb3031b73f812c012 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:GL000195.1 LN:182896 M5:5d9ec007868d517e73543b005ba48535 UR:file:/work/gencode/GRCh38.p5.genome.fa
@SQ SN:GL000205.2 LN:185591 M5:458e71cd53dd1df4083dc7983a6c82c4 UR:file:/work/gencode/GRCh38.p5.genome.fa

Interestingly after sorting my COSMIC vcf, all of my known contigs moves BEHIND all the unplaced contigs
##### ERROR cosmic contigs = [GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000208.1, GL000209.2, GL000213.1, GL000214.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, GL000226.1, GL000250.2, GL000251.2, GL000252.2, ... ... ... ... chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY]

ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2,... ... ...

Is this possibly because my dictionary is unsorted?

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