Duplicate columns in ReadLengthDistribution

lindenblindenb FranceMember ✭✭
edited September 2016 in Ask the GATK team

Hi GATK team,
I've run the following command:

java -jar gatk/3.6.0/GenomeAnalysisTK.jar -T ReadLengthDistribution -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37.fasta -L "2:237200000-237210000" -o out.txt  -I  bam.list -rf NotPrimaryAlignment -rf UnmappedRead -rf FailsVendorQualityCheck -rf DuplicateRead

in out.txt: the header starts with

#:GATKTable:ReadLengthDistribution:Table of read length distributions
readLength  10H0268  12H0162  12H0162  12H0300  12H0300  12H0356  10H0192  10H0027  10H0027  11H0493  11H0493  14H0292  13H0199  12H0447  12H0447  12H0031  12H0031  11H0404  11H0404  10H0227  12H0473  10H0469  14H0292  10H0469  13H0490  13H0490  13H0025  13H0025  12H0341  12H0341  12H0098  12H0098  12H0604  12H0604

as you can see, there are some duplicate columns e.g:12H0300 (wich don't always have the same value in the table.

my bam.list contains only 20 bam:

$ wc  bam.list 
  20   20 2520 bam.list

looking at the BAM headers, I can see that there are some samples that have more than one read-grou

$ cat  bam.list  | while read F; do echo "###"; samtools view -H "${F}" | grep "^@RG" ; done 
@RG ID:p20  PL:ILLUMINA PU:1    LB:13H0199  SM:13H0199
@RG ID:p12  PL:ILLUMINA PU:1    LB:12H0300  SM:12H0300
@RG ID:p13  PL:ILLUMINA PU:1    LB:12H0300  SM:12H0300
@RG ID:p21  PL:ILLUMINA PU:1    LB:12H0447  SM:12H0447
@RG ID:p22  PL:ILLUMINA PU:1    LB:12H0447  SM:12H0447

I suppose ReadLengthDistribution group the data by group ID and display the SM tag. Am I right ? Do you consider this as a bug or as a feature ? :-)
Is there a way to group the data by SM ?


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