@HD tag is missing in Aligned.toTranscriptome.out.bam even with outSAMheaderHD in run command

[Stikus]

Hello, thanks for great tool.

We are using STAR both for regular and transcriptome bams and transcriptome bam missing @HD tad in header:

root@688c610419c8:/outputs# samtools view -H S1_L001_R_STAR099_step4/S1_L001_R_step4.Aligned.sortedByCoord.out.bam | head
@HD     VN:1.6  SO:coordinate
@SQ     SN:chr1 LN:248956422
@SQ     SN:chr2 LN:242193529
@SQ     SN:chr3 LN:198295559
@SQ     SN:chr4 LN:190214555
@SQ     SN:chr5 LN:181538259
@SQ     SN:chr6 LN:170805979
@SQ     SN:chr7 LN:159345973
@SQ     SN:chr8 LN:145138636
@SQ     SN:chr9 LN:138394717

root@688c610419c8:/outputs# samtools view -H S1_L001_R_STAR099_step4/S1_L001_R_step4.Aligned.toTranscriptome.out.bam | head
@SQ     SN:ENST00000456328.2    LN:1657
@SQ     SN:ENST00000450305.2    LN:632
@SQ     SN:ENST00000488147.1    LN:1351
@SQ     SN:ENST00000619216.1    LN:68
@SQ     SN:ENST00000473358.1    LN:712
@SQ     SN:ENST00000469289.1    LN:535
@SQ     SN:ENST00000607096.1    LN:138
@SQ     SN:ENST00000417324.1    LN:1187
@SQ     SN:ENST00000461467.1    LN:590
@SQ     SN:ENST00000606857.1    LN:840

root@688c610419c8:/outputs# samtools view -H S1_L001_R_STAR099_step4/S1_L001_R_step4.Aligned.sortedByCoord.out.bam | grep '^@HD'
@HD     VN:1.6  SO:coordinate
root@688c610419c8:/outputs# samtools view -H S1_L001_R_STAR099_step4/S1_L001_R_step4.Aligned.toTranscriptome.out.bam | grep '^@HD'
root@688c610419c8:/outputs#

STAR run command:

$STAR --runThreadN $PROGRAMNUMCPUS --genomeLoad NoSharedMemory --limitBAMsortRAM $((memBytes*90/100)) $starIntIndexStr --readFilesIn $fastq1 $fastq2 $starReadCmdFlag --outFileNamePrefix $step4pref --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --alignIntronMax 500000 --alignMatesGapMax 1000000 --sjdbScore 2 --alignSJDBoverhangMin 1 --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --sjdbOverhang $((maxReadLength-1)) --quantMode TranscriptomeSAM --quantTranscriptomeSAMoutput BanSingleEnd --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN:1.6 --outSAMattrRGline ID:$RGID  LB:$library  PL:$platform  PU:$machine  SM:$sampleName