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chopdgd / bfx-tools-wdl

WDL tasks for commonly used BFX tools
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M5 info in BAM file from novoalign V5 #160

Closed weixuanfu closed 3 years ago

weixuanfu commented 3 years ago

For UI issues

Description

Novoalign V4, M5 information was added to bam file by default while Novoalign V3 did not add this information. The M5 info caused an issue in call-BAMQualityControl task in GermlinePanel pipeline. The CollectHsMetrics in picard will check if the M5 info in bam file is matched with intervals files's M5 info. It will raise a error if not matched.

What I Did

#V4's bam file

samtools view -H MASKED_ID.markdups.bam  | head -n 5
@HD VN:1.5  SO:coordinate
@SQ SN:1    LN:249250621    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:2    LN:243199373    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix M5:a0d9851da00400dec1098a9255ac712e
@SQ SN:3    LN:198022430    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix M5:fdfd811849cc2fadebc929bb925902e5
@SQ SN:4    LN:191154276    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix M5:23dccd106897542ad87d2765d28a19a1

#V3's bam file

samtools view -H MASKED_ID.markdups.bam | head -n 5
@HD VN:1.5  SO:coordinate
@SQ SN:1    LN:249250621    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix
@SQ SN:2    LN:243199373    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix
@SQ SN:3    LN:198022430    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix
@SQ SN:4    LN:191154276    AS:human_g1k_v37_MASKED_IKBKGP1_new.nix