Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MergeBamAlignment outputting all mapped and unmapped records #1778

Open
1 task done
stkgo opened this issue Feb 18, 2022 · 1 comment
Open
1 task done

MergeBamAlignment outputting all mapped and unmapped records #1778

stkgo opened this issue Feb 18, 2022 · 1 comment

Comments

@stkgo
Copy link

stkgo commented Feb 18, 2022

Bug Report

Affected tool(s)

MergeBamAlignment

Affected version(s)

  • GATK 4.2.3.0

Description

When provided with an unmapped BAM and a mapped BAM MergeBamAlignment returns all of the records instead of just the mapped records.

Steps to reproduce

This can be reproduced by running MergeBamAlignment with the following example reads.

Unmapped reads:

Solexa-272222:1089771	77	*	0	0	*	*	0	0	AGTGCTGGGATTACAGGCGTGNGCCNCCATGCCCNGCCCAGTATCATCCCTTTCAGTGACAGACNTTAGAGAGCACGGATTGGATTGATGCNGTAATGTCTCACCTCTCTGTCTCGCTCTGTTTTGGATAGCCGCATGTGCC	ijjjjjjjjjjjjjjjjjjjj#ijj#jjjjjjjj#jjjjjjjjjjjjjjjijjjjjjjjjjjjj#jjijjjjjijjjjjjjijjjjjjjjj#ijjjjjijjjjjjjjjjjijjjjijjjjjjijjjjjjjjjjjjjjijjji	aD:i:4	bD:i:1	cD:i:5	aE:f:0	bE:f:0	cE:f:0	RG:Z:A	MI:Z:1089771	aM:i:2	bM:i:0	cM:i:3	RX:Z:ACGACTTG-GTCGAAGA	ac:Z:AGTGCTGGGATTACAGGCGTGAGCCACCATGCCCAGCCCAGTATCATCCCTTTCAGTGACAGACTTTAGAGAGCACGGATTGGATTGATGCAGTAATGTCTCACCTCTCTGTCTCGCTCTGTTTTGGATAGCCGCATGTGCC	bc:Z:AGTGCTGGGATTACAGGCGTGNGCCNCCATGCCCNGCCCAGTATCATCCCTTTCAGTGACAGACNTTAGAGAGCACGGATTGGATTGATGCNGTAATGTCTCACCTCTCTGTCTCGCTCTGTTTTGGATAGCCGCATGTGCC	ad:B:s,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,3,2	bd:B:s,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	ae:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0	be:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0	aq:Z:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNM	bq:Z:<====================!<==!========!===============<=============!==<=====<=======<=========!<=====<===========<====<======<==============<====
Solexa-272222:1089771	141	*	0	0	*	*	0	0	AGATGCTTCGGCACATGCGGCTATCCAAANCAGAGCGAGACAGAGAGGTGAGACATTACTGCATCAATCCAATCCGTGCTCTCTAAAGTCTNTCACTGAAAGGGANGATACTGGGCTGGGCATGGTGGCTCACGNCTGTAATC	jjijjjjjjjjjijjjjjjjjijjjjjjj#jjjjijjjjjjjjjjjjjjjjjjjjjjjjjjjijjjjjjijjjjjjjjjjjjjjjjjjjjj#jjijjjjijjjjj#jjjjjjjjijjjjjjjjjjjjjijjijj#jjijjjji	aD:i:4	bD:i:1	cD:i:5	aE:f:0	bE:f:0	cE:f:0	RG:Z:A	MI:Z:1089771	aM:i:2	bM:i:0	cM:i:3	RX:Z:ACGACTTG-GTCGAAGA	ac:Z:AGATGCTTCGGCACATGCGGCTATCCAAAACAGAGCGAGACAGAGAGGTGAGACATTACTGCATCAATCCAATCCGTGCTCTCTAAAGTCTGTCACTGAAAGGGATGATACTGGGCTGGGCATGGTGGCTCACGCCTGTAATC	bc:Z:AGATGCTTCGGCACATGCGGCTATCCAAANCAGAGCGAGACAGAGAGGTGAGACATTACTGCATCAATCCAATCCGTGCTCTCTAAAGTCTNTCACTGAAAGGGANGATACTGGGCTGGGCATGGTGGCTCACGNCTGTAATC	ad:B:s,4,4,3,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,3,4,3,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,3,4,3,3,4,3,4,4,4,4,2,4,4,3,3,4,3,3,4,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,3,2,3,4,4,3,3,4,4,4,3,4,4,4,4,3,3,4,4,4,3,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,2,4,4,4,4,4,4,4,4,3,4,4	bd:B:s,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1	ae:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0	be:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0	aq:Z:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNMNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNMNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNMNNNNNNNNNNN	bq:Z:==<=========<========<=======!====<==================================<=====================!=======<=====!========<=============<=====!==<====<

Mapped reads:

Solexa-272222:1089771	99	chr15	34184835	0	16M51769N126M	=	34236612	151	AGTGCTGGGATTACAGGCGTGNGCCNCCATGCCCNGCCCAGTATCATCCCTTTCAGTGACAGACNTTAGAGAGCACGGATTGGATTGATGCNGTAATGTCTCACCTCTCTGTCTCGCTCTGTTTTGGATAGCCGCATGTGCC	ijjjjjjjjjjjjjjjjjjjj#ijj#jjjjjjjj#jjjjjjjjjjjjjjjijjjjjjjjjjjjj#jjijjjjjijjjjjjjijjjjjjjjj#ijjjjjijjjjjjjjjjjijjjjijjjjjjijjjjjjjjjjjjjjijjji	AS:i:-19	ZS:i:-19	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:21A3A8A29T26A50	YS:i:-10	YT:Z:CP	XS:A:+	NH:i:2
Solexa-272222:1089771	147	chr15	34236612	0	143M	=	34184835	-151	GATTACAGNCGTGAGCCACCATGCCCAGCCCAGTATCNTCCCTTTCAGTGANAGACTTTAGAGAGCACGGATTGGATTGATGCAGTAATGTCTCACCTCTCTGTCTCGCTCTGNTTTGGATAGCCGCATGTGCCGAAGCATCT	ijjjjijj#jjijjijjjjjjjjjjjjjijjjjjjjj#jjjjjijjjjijj#jjjjjjjjjjjjjjjjjjjjjijjjjjjijjjjjjjjjjjjjjjjjjjjjjjjjjjijjjj#jjjjjjjijjjjjjjjijjjjjjjjjijj	AS:i:-10	ZS:i:-20	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:8G28A13C61T21G7	YS:i:-19	YT:Z:CP	XS:A:+	NH:i:2
Solexa-272222:1089771	355	chr15	34185232	0	16M51372N126M	=	34236612	151	AGTGCTGGGATTACAGGCGTGNGCCNCCATGCCCNGCCCAGTATCATCCCTTTCAGTGACAGACNTTAGAGAGCACGGATTGGATTGATGCNGTAATGTCTCACCTCTCTGTCTCGCTCTGTTTTGGATAGCCGCATGTGCC	ijjjjjjjjjjjjjjjjjjjj#ijj#jjjjjjjj#jjjjjjjjjjjjjjjijjjjjjjjjjjjj#jjijjjjjijjjjjjjijjjjjjjjj#ijjjjjijjjjjjjjjjjijjjjijjjjjjijjjjjjjjjjjjjjijjji	AS:i:-19	ZS:i:-19	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:21A3A8A29T26A50	YS:i:-10	YT:Z:CP	XS:A:+	NH:i:2
Solexa-272222:1089771	403	chr15	34236612	0	143M	=	34185232	-151	GATTACAGNCGTGAGCCACCATGCCCAGCCCAGTATCNTCCCTTTCAGTGANAGACTTTAGAGAGCACGGATTGGATTGATGCAGTAATGTCTCACCTCTCTGTCTCGCTCTGNTTTGGATAGCCGCATGTGCCGAAGCATCT	ijjjjijj#jjijjijjjjjjjjjjjjjijjjjjjjj#jjjjjijjjjijj#jjjjjjjjjjjjjjjjjjjjjijjjjjjijjjjjjjjjjjjjjjjjjjjjjjjjjjijjjj#jjjjjjjijjjjjjjjijjjjjjjjjijj	AS:i:-10	ZS:i:-20	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:8G28A13C61T21G7	YS:i:-19	YT:Z:CP	XS:A:+	NH:i:2

Expected behavior

I would expect a BAM with the 4 mapped reads.

Actual behavior

I get a BAM with all 6 reads.

@stkgo
Copy link
Author

stkgo commented Feb 18, 2022

I think this might be the same issue as #589. The last two reads in my mapped reads example are not primary alignments, based on the SAM flags.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant