Question

GATK: Input files reads and reference have incompatible contigs: No overlapping contigs found

1

Entering edit mode

9.5 years ago

kumbarov ▴ 10

Hi,

I am trying to generate VCF file from a BAM file from FamilyTreeDNA. I run the following command:

java -Xmx2g -jar GenomeAnalysisTK.jar \
  -l INFO \
  -R resources/Homo_sapiens_assembly19.fasta \
  -T UnifiedGenotyper \
  -I /tmp/0209.sorted.bam \
  -L Y \
  -rf BadCigar \
  -o 0209.vcf \
  --output_mode EMIT_ALL_CONFIDEN

This is the error I get:

ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found.

I searched the forums and figured out it is due to mismatching reference and BAM file headers. This is my BAM file header:

SN:chrM
SN:chr1
SN:chr2
SN:chr3
SN:chr4
SN:chr5
SN:chr6
SN:chr7
SN:chr8
SN:chr9
SN:chr10
SN:chr11
SN:chr12
SN:chr13
SN:chr14
SN:chr15
SN:chr16
SN:chr17
SN:chr18
SN:chr19
SN:chr20
SN:chr21
SN:chr22
SN:chrX
SN:chrY
SN:chr1_gl000191_random
SN:chr1_gl000192_random
SN:chr4_ctg9_hap1
SN:chr4_gl000193_random
SN:chr4_gl000194_random
SN:chr6_apd_hap1
SN:chr6_cox_hap2
SN:chr6_dbb_hap3
SN:chr6_mann_hap4
SN:chr6_mcf_hap5
SN:chr6_qbl_hap6
SN:chr6_ssto_hap7
SN:chr7_gl000195_random
SN:chr8_gl000196_random
SN:chr8_gl000197_random
SN:chr9_gl000198_random
SN:chr9_gl000199_random
SN:chr9_gl000200_random
SN:chr9_gl000201_random
SN:chr11_gl000202_random
SN:chr17_ctg5_hap1
SN:chr17_gl000203_random
SN:chr17_gl000204_random
SN:chr17_gl000205_random
SN:chr17_gl000206_random
SN:chr18_gl000207_random
SN:chr19_gl000208_random
SN:chr19_gl000209_random
SN:chr21_gl000210_random
SN:chrUn_gl000211
SN:chrUn_gl000212
SN:chrUn_gl000213
SN:chrUn_gl000214
SN:chrUn_gl000215
SN:chrUn_gl000216
SN:chrUn_gl000217
SN:chrUn_gl000218
SN:chrUn_gl000219
SN:chrUn_gl000220
SN:chrUn_gl000221
SN:chrUn_gl000222
SN:chrUn_gl000223
SN:chrUn_gl000224
SN:chrUn_gl000225
SN:chrUn_gl000226
SN:chrUn_gl000227
SN:chrUn_gl000228
SN:chrUn_gl000229
SN:chrUn_gl000230
SN:chrUn_gl000231
SN:chrUn_gl000232
SN:chrUn_gl000233
SN:chrUn_gl000234
SN:chrUn_gl000235
SN:chrUn_gl000236
SN:chrUn_gl000237
SN:chrUn_gl000238
SN:chrUn_gl000239
SN:chrUn_gl000240
SN:chrUn_gl000241
SN:chrUn_gl000242
SN:chrUn_gl000243
SN:chrUn_gl000244
SN:chrUn_gl000245
SN:chrUn_gl000246
SN:chrUn_gl000247
SN:chrUn_gl000248
SN:chrUn_gl000249

And this is my dict file:

SN:1
SN:2
SN:3
SN:4
SN:5
SN:6
SN:7
SN:8
SN:9
SN:10
SN:11
SN:12
SN:13
SN:14
SN:15
SN:16
SN:17
SN:18
SN:19
SN:20
SN:21
SN:22
SN:X
SN:Y
SN:MT
SN:GL000207.1
SN:GL000226.1
SN:GL000229.1
SN:GL000231.1
SN:GL000210.1
SN:GL000239.1
SN:GL000235.1
SN:GL000201.1
SN:GL000247.1
SN:GL000245.1
SN:GL000197.1
SN:GL000203.1
SN:GL000246.1
SN:GL000249.1
SN:GL000196.1
SN:GL000248.1
SN:GL000244.1
SN:GL000238.1
SN:GL000202.1
SN:GL000234.1
SN:GL000232.1
SN:GL000206.1
SN:GL000240.1
SN:GL000236.1
SN:GL000241.1
SN:GL000243.1
SN:GL000242.1
SN:GL000230.1
SN:GL000237.1
SN:GL000233.1
SN:GL000204.1
SN:GL000198.1
SN:GL000208.1
SN:GL000191.1
SN:GL000227.1
SN:GL000228.1
SN:GL000214.1
SN:GL000221.1
SN:GL000209.1
SN:GL000218.1
SN:GL000220.1
SN:GL000213.1
SN:GL000211.1
SN:GL000199.1
SN:GL000217.1
SN:GL000216.1
SN:GL000215.1
SN:GL000205.1
SN:GL000219.1
SN:GL000224.1
SN:GL000223.1
SN:GL000195.1
SN:GL000212.1
SN:GL000222.1
SN:GL000200.1
SN:GL000193.1
SN:GL000194.1
SN:GL000225.1
SN:GL000192.1
SN:NC_007605

How can I get this to work or where can I find a suitable hg19 reference? My current reference is from ftp://ftp.ncbi.nlm.nih.gov/sra/reports/Assembly/GRCh37-HG19_Broad_variant/

bam gatk • 11k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by kumbarov ▴ 10

2

Entering edit mode

9.5 years ago

Pierre Lindenbaum 164k

How can I get this to work ?

Fool the tools using a symbolic link (usually a bad idea): http://plindenbaum.blogspot.fr/2011/10/reference-genome-with-or-without-chr.html

Where can I find a suitable hg19 reference?

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

I actually have conversion files for cases like this: https://github.com/dpryan79/ChromosomeMappings/blob/master/GRCh37_UCSC2ensembl.txt

ADD REPLY • link 9.5 years ago by Devon Ryan 104k

1

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9.5 years ago

Devon Ryan 104k

You appear to have mapped against the UCSC reference, so download the most recent GRCh37 patch set from there.

ADD COMMENT • link 9.5 years ago by Devon Ryan 104k

Ram · Accepted Answer · 2015-06-12

1

Entering edit mode

9.5 years ago

kumbarov ▴ 10

Editing the dict and fai files is cumbersome. I tried the following:

java -Xmx2g -jar GenomeAnalysisTK.jar -l INFO -R resources/chrY.fa \
     -T UnifiedGenotyper -I ${TMPDIR}/${NAME}.sorted.bam -L chrY \
     -rf BadCigar -o vcf_out/${NAME}.vcf --output_mode EMIT_ALL_CONFIDENT_SITES \
     -U ALLOW_SEQ_DICT_INCOMPATIBILITY

But I got an empty VCF file. How can I use a chrY.fa file only and get a VCF file with reference allele and genotype allele?

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by kumbarov ▴ 10

0

Entering edit mode

Why edit the dict file, just make a new one from the right fasta file.

ADD REPLY • link updated 23 months ago by Ram 44k • written 9.5 years ago by Devon Ryan 104k

0

Entering edit mode

Where is the correct file? Here I find only single chromosome files http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/

ADD REPLY • link updated 23 months ago by Ram 44k • written 9.5 years ago by kumbarov ▴ 10

0

Entering edit mode

just cat the files....

ADD REPLY • link updated 23 months ago by Ram 44k • written 9.5 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

cat worked. The catch was to cat the files in the correct order.

ADD REPLY • link updated 23 months ago by Ram 44k • written 9.5 years ago by kumbarov ▴ 10