Hello,
I was running:
java -jar picard.jar GenotypeConcordance -CALL_VCF new.vcf -CALL_SAMPLE 0_fam0110_G110 -O gc_concordance.vcf -TRUTH_VCF old.vcf -TRUTH_SAMPLE 0_fam0110_G110
and I got this error:
; Provider GCS is not available; Picard version: Version:2.23.3 [Wed Sep 02 20:01:28 CDT 2020] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2020081664 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 0 don't match: 0/247185616/1 0/249139234/1 at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:272) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:334) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:320) at picard.vcf.GenotypeConcordance.doWork(GenotypeConcordance.java:344) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:301) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
java -version
openjdk version "1.8.0_161"
OpenJDK Runtime Environment (build 1.8.0_161-b14)
OpenJDK 64-Bit Server VM (build 25.161-b14, mixed mode)
Can someone please tell me how to resolve this issue?
I also tried calculating concordance between those two .vcf files via:
java -jar SnpSift.jar concordance -v old.vcf new.vcf > concordance.txt
I transposed the results and for one sample I am getting this:
sample MISSING_ENTRY_old.MISSING_ENTRY_new
0_fam6013_G6013 0
MISSING_ENTRY_old.MISSING_GT_new MISSING_ENTRY_old.REF
0 899539
MISSING_ENTRY_old.ALT_1 MISSING_ENTRY_old.ALT_2
743281 232363
MISSING_GT_old.MISSING_ENTRY_new MISSING_GT_old.MISSING_GT_new
0 0
MISSING_GT_old.REF MISSING_GT_old.ALT_1
0 0
MISSING_GT_old.ALT_2 REF.MISSING_ENTRY_new
0 1603978
REF.MISSING_GT_new REF.REF
0 96
REF.ALT_1 REF.ALT_2
73 14
ALT_1.MISSING_ENTRY_new ALT_1.MISSING_GT_new
766721 0
ALT_1.REF ALT_1.ALT_1
34 39
ALT_1.ALT_2 ALT_2.MISSING_ENTRY_new
11 172654
ALT_2.MISSING_GT_new ALT_2.REF
0 9
ALT_2.ALT_1 ALT_2.ALT_2
5 4
ERROR
1684
Can you please help me understand what does this output tells about difference of my sample 0_fam6013_G6013 in old and new vcf, which are the key parameters to look for and is there is any way to visualize this?
•
written
by
anamaria
3 answers
Hi @anamaria. Did you ever figure out how to interpret the output of the concordance SNPSift output files?
Just sharing another possible solution using Python API with the pyvcf.compare method I wrote:
>>> from fuc import pyvcf
>>> data = {
... 'CHROM': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1'],
... 'POS': [100, 101, 102, 103, 104],
... 'ID': ['.', '.', '.', '.', '.'],
... 'REF': ['G', 'CT', 'T', 'C', 'A'],
... 'ALT': ['A', 'C', 'A', 'T', 'G,C'],
... 'QUAL': ['.', '.', '.', '.', '.'],
... 'FILTER': ['.', '.', '.', '.', '.'],
... 'INFO': ['.', '.', '.', '.', '.'],
... 'FORMAT': ['GT', 'GT', 'GT', 'GT', 'GT'],
... 'A': ['0/1', '0/0', '0/0', '0/1', '0/0'], # "Test" sample
... 'B': ['1/1', '0/1', './.', '0/1', '0/0'], # "Truth" sample
... }
>>> vf = pyvcf.VcfFrame.from_dict([], data)
>>> # vf = pyvcf.VcfFrame.from_file('in.vcf')
>>> vf.df
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
0 chr1 100 . G A . . . GT 0/1 1/1
1 chr1 101 . CT C . . . GT 0/0 0/1
2 chr1 102 . T A . . . GT 0/0 ./.
3 chr1 103 . C T . . . GT 0/1 0/1
4 chr1 104 . A G,C . . . GT 0/0 0/0
>>> # Return (Ab, aB, AB, ab) == (FP, FN, TP, TN)
>>> vf.compare('A', 'B', mode='all')
(0, 1, 2, 1)
>>> vf.compare('A', 'B', mode='snv')
(0, 0, 2, 1)
>>> vf.compare('A', 'B', mode='indel')
(0, 1, 0, 0)
Can someone please tell me how to resolve this issue?
you're comparing two VCFs that were not called with the very same reference.
See the lines starting with ##contig= in both VCF header.
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