Question

Annotate merged vcfs

0

Entering edit mode

6.2 years ago

Gene_MMP8 ▴ 240

I have 10 normal/tumor samples and I did the following:-
1. Generated vcfs
2. Normalised them
3. Merged together
Now I want to annotate the merged vcf, using java -Xmx4g -jar snpEff.jar -v -stats ex1.html GRCm38.75 finalMerge.vcf > final.anno.vcf
but I am getting an error

00:00:00    SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00    Command: 'ann'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'GRCm38.75'
00:00:00    Reading config file: /media/shayantanbanerjee/disk1/20_cancer_samples/dfata/snpEff/snpEff.config
00:00:00    done
00:00:00    Reading database for genome version 'GRCm38.75' from file '/media/shayantanbanerjee/disk1/20_cancer_samples/dfata/snpEff/./data/GRCm38.75/snpEffectPredictor.bin' (this might take a while)
00:00:09    done
00:00:09    Loading Motifs and PWMs
00:00:09    Building interval forest
00:00:12    done.
00:00:12    Genome stats :
#-----------------------------------------------
# Genome name                : 'Mus_musculus'
# Genome version             : 'GRCm38.75'
# Genome ID                  : 'GRCm38.75[0]'
# Has protein coding info    : true
# Has Tr. Support Level info : true
# Genes                      : 39179
# Protein coding genes       : 23232
#-----------------------------------------------
# Transcripts                : 94929
# Avg. transcripts per gene  : 2.42
# TSL transcripts            : 0
#-----------------------------------------------
# Checked transcripts        : 
#               AA sequences :  52148 ( 99.75% )
#              DNA sequences :  82932 ( 87.36% )
#-----------------------------------------------
# Protein coding transcripts : 52278
#              Length errors :   4872 ( 9.32% )
#  STOP codons in CDS errors :     40 ( 0.08% )
#         START codon errors :   4814 ( 9.21% )
#        STOP codon warnings :   3254 ( 6.22% )
#              UTR sequences :  48094 ( 50.66% )
#               Total Errors :   8962 ( 17.14% )
#-----------------------------------------------
# Cds                        : 432486
# Exons                      : 628052
# Exons with sequence        : 628052
# Exons without sequence     : 0
# Avg. exons per transcript  : 6.62
# WARNING!                   : Mitochondrion chromosome 'MT' does not have a mitochondrion codon table (codon table = 'Standard'). You should update the config file.
#-----------------------------------------------
# Number of chromosomes      : 80
# Chromosomes                : Format 'chromo_name size codon_table'
#       '1' 195471971   Standard
#       '2' 182113224   Standard
#       'MG4214_PATCH'  171031749   Standard
#       'X' 171031299   Standard
#       '3' 160039680   Standard
#       '4' 156508116   Standard
#       'MG4136_PATCH'  156508116   Standard
#       'MG4212_PATCH'  151862668   Standard
#       '5' 151834684   Standard
#       '6' 149736546   Standard
#       '7' 145441459   Standard
#       'MG4151_PATCH'  145439975   Standard
#       '10'    130694993   Standard
#       '8' 129401213   Standard
#       '14'    124902244   Standard
#       '9' 124595110   Standard
#       'MG132_PATCH'   124595110   Standard
#       '11'    122082543   Standard
#       'MG3829_PATCH'  122082543   Standard
#       '13'    120421639   Standard
#       'MG4180_PATCH'  120129530   Standard
#       '12'    120129022   Standard
#       '15'    104043685   Standard
#       'MG3833_PATCH'  98208653    Standard
#       '16'    98207768    Standard
#       '17'    94987271    Standard
#       'MG4222_MG3908_PATCH'   94987243    Standard
#       'MG4211_PATCH'  91797447    Standard
#       'MG4209_PATCH'  91793962    Standard
#       'Y' 91744698    Standard
#       'MG4213_PATCH'  91736668    Standard
#       'MG3835_PATCH'  90835696    Standard
#       '18'    90702639    Standard
#       '19'    61431566    Standard
#       'MG153_PATCH'   61431565    Standard
#       'JH584299.1'    953012  Standard
#       'GL456233.1'    336933  Standard
#       'JH584301.1'    259875  Standard
#       'GL456211.1'    241735  Standard
#       'GL456350.1'    227966  Standard
#       'JH584293.1'    207968  Standard
#       'GL456221.1'    206961  Standard
#       'JH584297.1'    205776  Standard
#       'JH584296.1'    199368  Standard
#       'GL456354.1'    195993  Standard
#       'JH584294.1'    191905  Standard
#       'JH584298.1'    184189  Standard
#       'JH584300.1'    182347  Standard
#       'GL456219.1'    175968  Standard
#       'GL456210.1'    169725  Standard
#       'JH584303.1'    158099  Standard
#       'JH584302.1'    155838  Standard
#       'GL456212.1'    153618  Standard
#       'JH584304.1'    114452  Standard
#       'GL456379.1'    72385   Standard
#       'GL456216.1'    66673   Standard
#       'GL456393.1'    55711   Standard
#       'GL456366.1'    47073   Standard
#       'GL456367.1'    42057   Standard
#       'GL456239.1'    40056   Standard
#       'GL456213.1'    39340   Standard
#       'GL456383.1'    38659   Standard
#       'GL456385.1'    35240   Standard
#       'GL456360.1'    31704   Standard
#       'GL456378.1'    31602   Standard
#       'GL456389.1'    28772   Standard
#       'GL456372.1'    28664   Standard
#       'GL456370.1'    26764   Standard
#       'GL456381.1'    25871   Standard
#       'GL456387.1'    24685   Standard
#       'GL456390.1'    24668   Standard
#       'GL456394.1'    24323   Standard
#       'GL456392.1'    23629   Standard
#       'GL456382.1'    23158   Standard
#       'GL456359.1'    22974   Standard
#       'GL456396.1'    21240   Standard
#       'GL456368.1'    20208   Standard
#       'MT'    16299   Standard
#       'JH584292.1'    14945   Standard
#       'JH584295.1'    1976    Standard
#-----------------------------------------------

00:00:14    Predicting variants
VcfFileIterator.parseVcfLine(132):  Fatal error reading file 'finalMerge.vcf' (line: 1):
�BC�4͝
         @�U����� 7AaDTn�0�g��"���xM�aC@@�j7ʴ{�����Vn��v�6�ֿ�\j�J�.[v�{�ٶV��<�}�y���3���lm���}���|�s��甕O����иq-m���e�^��)+s3u���M��i�l0�TW�-�f�W�z��ۺz�:;�ɖ�v-�T���G�e��5'�WW�3f��'{��z;;�{�����ٙ�L]aFnnnNAS3>���b�u4ٌp墬����e��.k{�ue�Ҭe�
java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
�BC�4͝
         @�U����� 7AaDTn�0�g��"���xM�aC@@�j7ʴ{�����Vn��v�6�ֿ�\j�J�.[v�{�ٶV��<�}�y���3���lm���}���|�s��甕O����иq-m���e�^��)+s3u���M��i�l0�TW�-�f�W�z��ۺz�:;�ɖ�v-�T���G�e��5'�WW�3f��'{��z;;�{�����ٙ�L]aFnnnNAS3>���b�u4ٌp墬����e��.k{�ue�Ҭe�
    at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:133)
    at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:184)
    at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:57)
    at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:467)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:142)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1029)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
�BC�4͝
         @�U����� 7AaDTn�0�g��"���xM�aC@@�j7ʴ{�����Vn��v�6�ֿ�\j�J�.[v�{�ٶV��<�}�y���3���lm���}���|�s��甕O����иq-m���e�^��)+s3u���M��i�l0�TW�-�f�W�z��ۺz�:;�ɖ�v-�T���G�e��5'�WW�3f��'{��z;;�{�����ٙ�L]aFnnnNAS3>���b�u4ٌp墬����e��.k{�ue�Ҭe�
    at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1007)
    at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:219)
    at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:130)
    ... 9 more
00:00:14    Logging
00:00:15    Checking for updates...
00:00:16    Done.

sequencing next-gen • 2.5k views

ADD COMMENT • link updated 6.2 years ago by GenoMax 142k • written 6.2 years ago by Gene_MMP8 ▴ 240

0

Entering edit mode

Hello,

please post the first lines of you finalMerge.vcf. It looks like it isn't a real vcf file. It looks like there is something binary in it (bcf??)

fin swimmer

ADD REPLY • link 6.2 years ago by finswimmer 16k

0

Entering edit mode

Thanks for replying. The first lines of the vcf file are illegible too. Something like this \8B\00\00\00\00\00\FF\00BC\00\D04͝
The command used to merge the vcfs was: bcftools merge -Ob -m -any s1.vcf.gz s2.vcf.gz ..... > merge.vcf

ADD REPLY • link updated 6.2 years ago by GenoMax 142k • written 6.2 years ago by Gene_MMP8 ▴ 240

score 2 · Accepted Answer · 2018-03-08

2

Entering edit mode

6.2 years ago

finswimmer 16k

bcftools merge -Ob -m -any s1.vcf.gz s2.vcf.gz ..... > merge.vcf

With the -Ob option you create a compressed bcf file. I guess SnpEff cannot work with this file type.

Maybe you can use bcftools convert to get a vcf and stream the result directly to SnpEff. Or just use -Ov in your merge command for creating a normal vcf file.

fin swimmer

ADD COMMENT • link 6.2 years ago by finswimmer 16k

0

Entering edit mode

Thanks a lot. That worked like magic. Guess I was going wrong on the compressed file part.

ADD REPLY • link 6.2 years ago by Gene_MMP8 ▴ 240

0

Entering edit mode

Fine if I could help.

Please mark my answer as accepted. So everone can see that your problem is solved.

fin swimmer

ADD REPLY • link 6.2 years ago by finswimmer 16k