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**AnushaC** · 06-25-2014, 04:17 PM

I tried this header too
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:chr2 LN:243199373 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a0d9851da00400dec1098a9255ac712e
@SQ SN:chr3 LN:198022430 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:641e4338fa8d52a5b781bd2a2c08d3c3
@SQ SN:chr4 LN:191154276 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:23dccd106897542ad87d2765d28a19a1
@SQ SN:chr5 LN:180915260 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0740173db9ffd264d728f32784845cd7
@SQ SN:chr6 LN:171115067 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1d3a93a248d92a729ee764823acbbc6b
@SQ SN:chr7 LN:159138663 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:618366e953d6aaad97dbe4777c29375e
@SQ SN:chr8 LN:146364022 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:96f514a9929e410c6651697bded59aec
@SQ SN:chr9 LN:141213431 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:3e273117f15e0a400f01055d9f393768
@SQ SN:chr10 LN:135534747 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:988c28e000e84c26d552359af1ea2e1d
@SQ SN:chr11 LN:135006516 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98c59049a2df285c76ffb1c6db8f8b96
@SQ SN:chr12 LN:133851895 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:51851ac0e1a115847ad36449b0015864
@SQ SN:chr13 LN:115169878 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:283f8d7892baa81b510a015719ca7b0b
@SQ SN:chr14 LN:107349540 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98f3cae32b2a2e9524bc19813927542e
@SQ SN:chr15 LN:102531392 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:e5645a794a8238215b2cd77acb95a078
@SQ SN:chr16 LN:90354753 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:fc9b1a7b42b97a864f56b348b06095e6
@SQ SN:chr17 LN:81195210 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:351f64d4f4f9ddd45b35336ad97aa6de
@SQ SN:chr18 LN:78077248 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
@SQ SN:chr19 LN:59128983 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1aacd71f30db8e561810913e0b72636d
@SQ SN:chr20 LN:63025520 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0dec9660ec1efaaf33281c0d5ea2560f
@SQ SN:chr21 LN:48129895 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:2979a6085bfe28e3ad6f552f361ed74d
@SQ SN:chr22 LN:51304566 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a718acaa6135fdca8357d5bfe94211dd
@SQ SN:chrX LN:155270560 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:7e0e2e580297b7764e31dbc80c2540dd
@SQ SN:chrY LN:59373566 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1e86411d73e6f00a10590f976be01623
chr1 564490 564532 + target_1
chr1 564533 564534 + target_2
chr1 564672 564718 + target_3
chr1 564720 564721 + target_4
chr1 564722 564724 + target_5

**rbagnall** · 06-26-2014, 02:20 AM

GATK -L interval files do not need a header. They should be this format:

chr1:1000-1200
chr1:2004-2507
chr2:457290-457400

etc...

**bruce01** · 06-26-2014, 03:47 AM

Can also be tab separated:

Code:

CHR   POS1   POS2

**AnushaC** · 06-26-2014, 07:58 AM

It is not working I did like this
chr1:564490-564532 + target_1
chr1:564533-564534 + target_2
chr1:564672-564718 + target_3
chr1:564720-564721 + target_4
chr1:564722-564724 + target_5
chr1:564739-564741 + target_6
chr1:564771-564774 + target_7
chr1:564776-564807 + target_8
chr1:564898-564956 + target_9
chr1:564965-564966 + target_10
########################
##### ERROR MESSAGE: File associated with name /mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/intersectalltissues/hg19_lite_copy_HR5.interval_list is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: chr1:564490-564532 + target_1
##### ERROR --

**AnushaC** · 06-26-2014, 08:05 AM

chr1 564490 564532
chr1 564533 564534
chr1 564672 564718
chr1 564720 564721
chr1 564722 564724
chr1 564739 564741
chr1 564771 564774
chr1 564776 564807
##### ERROR MESSAGE: Badly formed genome loc: Contig 'chr1 564490 564532' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?
##### ERROR -----
I am used same reference fast file many times it worked fine .

**bruce01** · 06-26-2014, 08:08 AM

Are your chromosome names "chr1", "chr2", "chr3" etc?

They seem to be "chr2 LN:243199373" or something from previous posts.

You have to use the exact same chromosome naming format that is in the reference fasta. Otherwise the software cannot find the chromosome!

When I first encountered this error I made a fasta with chromosomes name "1", "2", "3" etc for ease of use. Might be an idea.

**AnushaC** · 06-26-2014, 08:15 AM

1 564490 564532 + target_1
1 564533 564534 + target_2
1 564672 564718 + target_3
1 564720 564721 + target_4
1 564722 564724 + target_5
1 564739 564741 + target_6
1 564771 564774 + target_7
1 564776 564807 + target_8
1 564898 564956 + target_9
1 564965 564966 + target_10

I tried like this too but did not work

**AnushaC** · 06-26-2014, 08:34 AM

@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:chr2 LN:243199373 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a0d9851da00400dec1098a9255ac712e
@SQ SN:chr3 LN:198022430 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:641e4338fa8d52a5b781bd2a2c08d3c3
@SQ SN:chr4 LN:191154276 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:23dccd106897542ad87d2765d28a19a1
@SQ SN:chr5 LN:180915260 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0740173db9ffd264d728f32784845cd7
@SQ SN:chr6 LN:171115067 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1d3a93a248d92a729ee764823acbbc6b
@SQ SN:chr7 LN:159138663 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:618366e953d6aaad97dbe4777c29375e
@SQ SN:chr8 LN:146364022 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:96f514a9929e410c6651697bded59aec
@SQ SN:chr9 LN:141213431 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:3e273117f15e0a400f01055d9f393768
@SQ SN:chr10 LN:135534747 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:988c28e000e84c26d552359af1ea2e1d
@SQ SN:chr11 LN:135006516 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98c59049a2df285c76ffb1c6db8f8b96
@SQ SN:chr12 LN:133851895 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:51851ac0e1a115847ad36449b0015864
@SQ SN:chr13 LN:115169878 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:283f8d7892baa81b510a015719ca7b0b
@SQ SN:chr14 LN:107349540 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98f3cae32b2a2e9524bc19813927542e
@SQ SN:chr15 LN:102531392 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:e5645a794a8238215b2cd77acb95a078
@SQ SN:chr16 LN:90354753 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:fc9b1a7b42b97a864f56b348b06095e6
@SQ SN:chr17 LN:81195210 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:351f64d4f4f9ddd45b35336ad97aa6de
@SQ SN:chr18 LN:78077248 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
@SQ SN:chr19 LN:59128983 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1aacd71f30db8e561810913e0b72636d
@SQ SN:chr20 LN:63025520 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0dec9660ec1efaaf33281c0d5ea2560f
@SQ SN:chr21 LN:48129895 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:2979a6085bfe28e3ad6f552f361ed74d
@SQ SN:chr22 LN:51304566 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a718acaa6135fdca8357d5bfe94211dd
@SQ SN:chrX LN:155270560 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:7e0e2e580297b7764e31dbc80c2540dd
@SQ SN:chrY LN:59373566 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1e86411d73e6f00a10590f976be01623
1 564490 564532 + target_1
1 564533 564534 + target_2
1 564672 564718 + target_3

It give me sth like this

WARNING 2014-06-26 09:32:07 IntervalList Ignoring interval for unknown reference: X:153990999-153991009
WARNING 2014-06-26 09:32:07 IntervalList Ignoring interval for unknown reference: X:153991010-153991011
WARNING 2014-06-26 09:32:07 IntervalList Ignoring interval for unknown reference: X:153991012-153991016
WARNING 2014-06-26 09:32:07 IntervalList Ignoring interval for unknown reference: Y:8979526-8979550
WARN 09:32:07,516 IntervalUtils - The interval file /mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/intersectalltissues/test.interval_list contains no intervals that could be parsed.
INFO 09:32:07,518 IntervalUtils - Processing 0 bp from intervals
WARN 09:32:07,520 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process.
INFO 09:32:07,611 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 09:32:07,614 GenomeAnalysisEngine - Done preparing for traversal

**bruce01** · 06-26-2014, 08:41 AM

Your reference chromosome names are: "chr1 LN:249250621" etc.

So make your interval file with those:

Code:

chr1	LN:249250621	564490	564532
chr1	LN:249250621	564533	564534
chr1	LN:249250621	564672	564718
chr1	LN:249250621	564720	564721

Unless you do this, GATK cannot parse the interval file.

**AnushaC** · 06-26-2014, 07:45 PM

achimmiri@idash-cloud-707:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/intersectalltissues$ head test1.subtract.interval_list
chr1 LN:249250621 564490 564532
chr1 LN:249250621 564533 564534
chr1 LN:249250621 564672 564718
chr1 LN:249250621 564720 564721
chr1 LN:249250621 564722 564724
I used this with and without header
t
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:chr2 LN:243199373 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a0d9851da00400dec1098a9255ac712e
@SQ SN:chr3 LN:198022430 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:641e4338fa8d52a5b781bd2a2c08d3c3
@SQ SN:chr4 LN:191154276 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:23dccd106897542ad87d2765d28a19a1
@SQ SN:chr5 LN:180915260 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0740173db9ffd264d728f32784845cd7

But still not working in any possible way.

**AnushaC** · 06-26-2014, 08:01 PM

I still not able to figure out what is the exact format for interval list . I tried every thing so far none of them worked . I checked my dict file my header is exactly same as dict filr
but I am not sure what does body part should look like .

**bruce01** · 06-27-2014, 01:10 AM

Just a moment...

http://gatkforums.broadinstitute.org/discussion/3395/interval-file-errors

Just a moment...

http://gatkforums.broadinstitute.org/discussion/2518/l-option-file-formats

http://www.broadinstitute.org/gatk/guide/article?id=1204

**QazSeDc** · 10-06-2016, 06:49 PM

I have run into the same exact problems!
I have been trying so many formats with different file suffix (.bed .list .intervals .interval_list) but only .bed and .interval_list worked for me so far.

.bed format:
<chr> <start> <end>

.interval_list format:
<chr>:<start>-<end>

However, since .bed is 0-based and .interval_list wouldn't allow any annotation after the interval on each line, I really want to get the .list format working.

I tried the gatk recommendation for .list format and even tried coping it but none worked for me.

I would like to know how did AnushaC end up solving this problem.

**QazSeDc** · 10-07-2016, 12:08 AM

so i decided to test out what format can be used and got the following results:

command:
java ../GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T DepthOfCoverage -I <in.bam> -R <hg19.fa> -L <test.list> --interval_merging OVERLAPPING_ONLY -o <out.file>
---------------------------------------------------------------------------------------
test1.list

chr1 69089 70010
chr1 367657 368599
chr1 621094 622036
chr1 861320 861395
chr1 865533 865718

test1 result:
##### ERROR MESSAGE: Badly formed genome loc: Contig 'chr1 69089 70010' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?
---------------------------------------------------------------------------------------
test2.list

chr1:69089-70010
chr1:367657-368599
chr1:621094-622036
chr1:861320-861395
chr1:865533-865718

test2 result:
no error message and all results have been correctly calculated.
---------------------------------------------------------------------------------------
test3.list (this format is recommended on the gatk website)

@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:chr2 LN:243199373 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:a0d9851da00400dec1098a9255ac712e
...
...
@SQ SN:chrUn_gl000248 LN:39786 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:5a8e43bec9be36c7b49c84d585107776
@SQ SN:chrUn_gl000249 LN:38502 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1d78abec37c15fe29a275eb08d5af236
chr1 69089 70010
chr1 367657 368599
chr1 621094 622036
chr1 861320 861395
chr1 865533 865718

test3 result:
##### ERROR
##### ERROR MESSAGE: File associated with name test3.list is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: @HD VN:1.0 SO:unsorted
---------------------------------------------------------------------------------------
test4.list

@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:chr2 LN:243199373 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:a0d9851da00400dec1098a9255ac712e
...
...
@SQ SN:chrUn_gl000248 LN:39786 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:5a8e43bec9be36c7b49c84d585107776
@SQ SN:chrUn_gl000249 LN:38502 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1d78abec37c15fe29a275eb08d5af236
chr1:69089-70010
chr1:367657-368599
chr1:621094-622036
chr1:861320-861395
chr1:865533-865718

test4 result:
##### ERROR MESSAGE: File associated with name test4.list is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: @HD VN:1.0 SO:unsorted
---------------------------------------------------------------------------------------
test5.list

chr1 69089 70010 + A
chr1 367657 368599 + B
chr1 621094 622036 + C
chr1 861320 861395 + D
chr1 865533 865718 + E

test5 result:
##### ERROR MESSAGE: Badly formed genome loc: Contig 'chr1 69089 70010 + A' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?
---------------------------------------------------------------------------------------
test6.list

chr1:69089-70010 + target1
chr1:367657-368599 + target2
chr1:621094-622036 + target3
chr1:861320-861395 + target4
chr1:865533-865718 + target5

test6 result:
##### ERROR MESSAGE: File associated with name test6.list is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: chr1:69089-70010 + target1
---------------------------------------------------------------------------------------
In test2 the format <chr>:<start>-<end> worked well as rbagnall mentioned:

Originally posted by rbagnall View Post

GATK -L interval files do not need a header. They should be this format:

chr1:1000-1200
chr1:2004-2507
chr2:457290-457400

etc...

However I would prefer using the format <chr> <start> <end> if possible for several reasons.
Overall i am not sure why test1 or test3 wouldn't work

sorry for the long post

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